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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kaptive">Debian Med / kaptive</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/881cad106df99d3ac0c55b764ae85d185b6aaeb5">881cad10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create changelog entry
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/e2df2e25e6cdb581167ed61812cda89328651594">e2df2e25</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:09:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/356ee2d6a6615f6d98011f8c1164404464c427ca">356ee2d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:09:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.7.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/07176d6259df963423c054b2e84a69d4e55f534a">07176d62</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.7.3'
Update to upstream version '0.7.3'
with Debian dir 4b12698d111ef173d3d8e1eae8a5b810189ca8d3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/acf7d644101e49330a16d55b033d96aee8f39752">acf7d644</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/ba3800a456d4207da7039372b8b416cd9ecf7ac2">ba3800a4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/fb17bda9540a2c8b29c863d69122e9035e898052">fb17bda9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/f4df80cd3fce5006d3069f85a4aa969edcbf3e58">f4df80cd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/b26123477e84ac04d7f17215dd24b9ee9645d284">b2612347</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:11:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Wrap long lines in changelog entries: 0.7.3-1.
Changes-By: lintian-brush
Fixes: lintian: debian-changelog-line-too-long
See-also: https://lintian.debian.org/tags/debian-changelog-line-too-long.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/fe5da3f33904423b3377406a2083e1b4027ec50b">fe5da3f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T07:59:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install wrapper script created by debhelper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/-/commit/5244f37e31e5276803be7af791794b887fb17b84">5244f37e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-13T08:00:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Override dh_missing to ignore egg-info
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#1642cefec3a60648eab36823f7a30dfd23d49231">
debian/kaptive.install
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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</a>
</li>
<li class="file-stats">
<a href="#9c2fb03a3a9d3ff211d09903fb3ed105bc81ec66">
kaptive.py
</a>
</li>
<li class="file-stats">
<a href="#5b4b74f94e5f5c673c13808c85115407ba2410c2">
reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk
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</li>
<li class="file-stats">
<a href="#b6a739f9e608d3a7bddc8e120bffa93d12a3c203">
reference_database/Klebsiella_k_locus_primary_reference.gbk
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</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Given a novel genome and a database of known loci (K, O or OC), Kaptive will hel</td>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">In cases where your input assembly closely matches a known locus, Kaptive should make that obvious. When your assembly has a novel type, that too should be clear. However, Kaptive cannot reliably extract or annotate locus sequences for totally novel types – if it indicates a novel locus is present then extracting and annotating the sequence is up to you! Very poor assemblies can confound the results, so be sure to closely examine any case where the locus sequence in your assembly is broken into multiple pieces.</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">If you think you have found a novel locus that should be added to one of the databases distributed with Kaptive please <span class="p">[</span><span class="nv" style="color: #008080;">contact us</span><span class="p">](</span><span class="sx" style="color: #d14;">mailto:kaptive.typing@gmail.com</span><span class="p">)</span>.</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="idiff left">Read more about Kaptive, Kaptive Web and the locus databases in </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">our papers</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">#citation</span></span><span class="p"><span class="idiff right">)</span></span>.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="idiff left">For citation info and details about Kaptive, Kaptive Web and the locus databases, see </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">our papers</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">#citation</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> below</span>.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Table of Contents</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +91,7 @@ kaptive.py -h</td>
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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Other dependencies</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown">Regardless of how you download/install Kaptive, it requires that <span class="p">[</span><span class="nv" style="color: #008080;">BLAST+</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/books/NBK279690/</span><span class="p">)</span> is available on the command line (specifically the commands <span class="sb" style="color: #d14;">`makeblastdb`</span>, <span class="sb" style="color: #d14;">`blastn`</span> and <span class="sb" style="color: #d14;">`tblastn`</span>). BLAST+ can usually be easily installed using a package manager such as <span class="p">[</span><span class="nv" style="color: #008080;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">on</span> Mac) or <span class="p">[</span><span class="nv" style="color: #008080;">apt-get</span><span class="p">](</span><span class="sx" style="color: #d14;">https://help.ubuntu.com/community/AptGet/Howto</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">on</span> Ubuntu and related Linux distributions).</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">Regardless of how you download/install Kaptive, it requires that <span class="p">[</span><span class="nv" style="color: #008080;">BLAST+</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/books/NBK279690/</span><span class="p">)</span> is available on the command line (specifically the commands <span class="sb" style="color: #d14;">`makeblastdb`</span>, <span class="sb" style="color: #d14;">`blastn`</span> and <span class="sb" style="color: #d14;">`tblastn`</span>). BLAST+ can usually be easily installed using a package manager such as <span class="p">[</span><span class="nv" style="color: #008080;">Homebrew</span><span class="p">](</span><span class="sx" style="color: #d14;">http://brew.sh/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">on</span> Mac) or <span class="p">[</span><span class="nv" style="color: #008080;">apt-get</span><span class="p">](</span><span class="sx" style="color: #d14;">https://help.ubuntu.com/community/AptGet/Howto</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">on</span> Ubuntu and related Linux distributions).<span class="idiff left right"> Some later versions of BLAST+ have been associated with sporadic crashes when running tblastn with multiple threads; to avoid this problem we recommend running Kaptive with BLAST+ v 2.3.0 or using the "--threads 1" option (see below for full command argument details).</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Input files</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -308,7 +308,18 @@ WARNING: If you use the variant database please inspect your results carefully a</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown">Database versions:</span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown"><span class="p">*</span> Kaptive releases v0.5.1 and below include the original _Klebsiella_ K locus databases, as described in <span class="p">[</span><span class="nv" style="color: #008080;">Wyres, K. et al. Microbial Genomics (2016).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000102</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.6.0 includes four novel primary _Klebsiella_ K locus references defined on the basis of gene content (KL162-KL165) in this <span class="p">[</span><span class="nv" style="color: #008080;">paper.</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.biorxiv.org/content/10.1101/557785v1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.6.0 and above include four novel primary _Klebsiella_ K locus references defined on the basis of gene content (KL162-KL165) in this <span class="p">[</span><span class="nv" style="color: #008080;">paper.</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.biorxiv.org/content/10.1101/557785v1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.1 and above contain updated versions of the KL53 and KL126 loci (see table below for details). The updated KL126 locus sequence will be described in McDougall, F. et al. 2020. _Klebsiella pneumoniae_ diversity and detection of _Klebsiella africana_ in Australian Fruit Bats (_Pteropus policephalus_). _In prep._</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.2 and above include a novel primary _Klebsiella_ K locus reference defined on the basis of gene content (KL166), which will be described in Li, M. et al. 2020. Characterization of clinically isolated hypermucoviscous _Klebsiella pneumoniae_ in Japan. _In prep._</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.3 and above include four novel primary _Klebsiella_ K locus references defined on the basis of gene content (KL167-KL170), which will be described in Gorrie, C. et al. 2020. Opportunity and diversity: A year of _Klebsiella pneumoniae_ infections in hospital. _In prep._</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown">Changes to the _Klebsiella_ K locus primary reference database:</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown">| Locus | Change | Reason | Date of change | Kaptive version no. |</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown">| ------------- | ------------- | ------------- | ------------- | ------------- |</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown">| KL53 | Annotation update: _wcaJ_ changed to _wbaP_ | Error in original annotation | 21 July 2020 | v 0.7.1 | </span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown">| KL126 | Sequence update: new sequence from isolate FF923 includes _rmlBADC_ genes between _gnd_ and _ugd_ | Assembly scaffolding error in original sequence from isolate A-003-I-a-1 | 21 July 2020 | v 0.7.1 |</span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### _Klebsiella_ O locus database</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -330,7 +341,7 @@ The _A. baumannii_ OC (lipooligosaccharide outer core) locus reference database</td>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="markdown">WARNING: These databases have been developed and tested specifically for _A. baumannii_ and may not be suitable for screening other _Acinetobacter_ species. You can check that your assembly is a true _A. baumannii_ by screening for the _oxaAB_ gene e.g. using blastn.</span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown"> Database versions:</span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.0 and above include the original _A. baumannii_ K and OC locus databases, as described in <span class="idiff left right">Wyres, KL. et al. _In prep_ 2019.</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown"><span class="p">*</span> Kaptive v0.7.0 and above include the original _A. baumannii_ K and OC locus databases, as described in <span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Wyres, KL. et al. Microbial Genomics, 2020.</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://doi.org/10.1099/mgen.0.000339</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -349,6 +360,21 @@ Kaptive uses 'tblastn' to screen for the presence of each locus gene with a cove</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="markdown">A small number of the original _Klebsiella_ K locus references are truncated, containing only a partial <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span> sequence. The reference annotations for these loci do not include <span class="nt" style="color: #000080;"><i></span>ugd<span class="nt" style="color: #000080;"></i></span>, so are not identified by the 'tblastn' search. Instead <span class="nt" style="color: #000080;"><b></span>Kaptive<span class="nt" style="color: #000080;"></b></span> reports the closest match to the partial sequence (if it exceeds the 90% coverage threshold). </span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Why has the best matching locus changed after I reran my analysis with an updated version of the database? ####</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="markdown">The databases are updated as novel loci are discovered and curated. If your previous match had a confidence call of 'Low' or 'None' but your new match has higher confidence, this indicates that your genome contains a locus that was absent in the older version of the database! So nothing to worry about here.</span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown">But what if your old match and your new match have 'Good' or better confidence levels?</span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="markdown">If your old match had 'Perfect' or 'Very High' confidence, please post an issue to the issues page, as this may indicate a problem with the new database!</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="markdown">If your old match had 'Good' or 'High' confidence please read on...</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown">Polysaccharide loci are subject to frequent recombinations and rearrangements, which generates new variants. As a result, a small number of pairs of loci share large regions of homology e.g. the _Klebsiella_ K-locus KL170 is very similar to KL101, and in fact seems to be a hybrid of KL101 plus a small region from KL106. </span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="markdown">Kaptive can accurately distinguish the KL101 and KL170 loci when it is working with high quality genome assemblies, but this task is much trickier if the assembly is fragmented. This means that matches to KL101 that were reported using an early version of the K-locus database might be reported as KL170 when using a later version of the database.</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="markdown">However, this should only occur in instances where the K-locus is fragmented in the genome assembly and in that case Kaptive will have indicated 'problems' with the matches (e.g. '?' indicating fragmented assembly or '-' indicating that an expected gene is missing), and the corresponding confidence level will be at the lower end of the scale (i.e. 'Good' or 'High', but not 'Very High' or 'Perfect').</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="markdown">You may want to try to figure out the correct locus manually, e.g. using <span class="p">[</span><span class="nv" style="color: #008080;">Bandage</span><span class="p">](</span><span class="sx" style="color: #d14;">https://rrwick.github.io/Bandage/</span><span class="p">)</span> to BLAST the corresponding loci in your genome assembly graph. </span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -359,7 +385,7 @@ If you use [Kaptive Web](http://kaptive.holtlab.net/) and/or the _Klebsiella_ O</td>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for _Klebsiella_ genomes. Journal of Clinical Microbiology (2018).</span><span class="p">](</span><span class="sx" style="color: #d14;">http://jcm.asm.org/content/56/6/e00197-18</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="markdown">If you use the _A. baumannii_ K or OC locus database(s) in your research please cite this paper:</span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="markdown"><span class="idiff left right">Identification of _Acinetobacter baumannii_ loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Wyres KL, Cahill SM, Holt KE, Hall RM and Kenyon JJ. _In preparation_.</span> </span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Identification of _Acinetobacter baumannii_ loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Microbial Genomics (2020).</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://doi.org/10.1099/mgen.0.000339</span></span><span class="p"><span class="idiff right">)</span></span> </span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="markdown">Lists of papers describing each of the individual _A. baumannii_ reference loci can be found <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/katholt/Kaptive/tree/master/extras</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kaptive (0.7.3-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Iain Lane ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/patches/blastdb_4: Pass "-blastdb_version 4" to makeblastdb to work</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> properly on 32 bit systems</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Install wrapper script created by debhelper</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Override dh_missing to ignore egg-info</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 13 Sep 2020 07:09:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">kaptive (0.7.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * More verbose test</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,15 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-biopython <!nocheck></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kaptive</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kaptive.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/katholt/Kaptive</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: kaptive</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: all</span>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#1642cefec3a60648eab36823f7a30dfd23d49231"><strong>debian/kaptive.install</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx"><span class="idiff left">kaptive</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nx"><span class="idiff">py</span></span><span class="idiff right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,3 +9,7 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> rm -rf Kaptive.egg-info</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_missing:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> find debian/tmp -type d -name Kaptive-0.7.3.egg-info | xargs rm -rf</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> dh_missing</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#9c2fb03a3a9d3ff211d09903fb3ed105bc81ec66"><strong>kaptive.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +52,7 @@ import random</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.<span class="idiff left right">5.1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.<span class="idiff left right">7.3</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<a href="https://salsa.debian.org/med-team/kaptive/-/compare/7505cc6b9d615269323acd6a88eb407a1f15b2a6...5244f37e31e5276803be7af791794b887fb17b84#5b4b74f94e5f5c673c13808c85115407ba2410c2"><strong>reference_database/Acinetobacter_baumannii_OC_locus_primary_reference.gbk</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1446,7 +1446,7 @@ FEATURES Location/Qualifiers</td>
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="plaintext"> /note="sequence from NCBI GenBank accession number</span>
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="plaintext"> KF030679 REGION: complement(28675..37977)"</span>
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="plaintext"> CDS 1..888</span>
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<pre style="margin: 0;">-<span id="LC1449" class="line" lang="plaintext"> /gene="gtrOC1"<span class="idiff left right">"</span></span>
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="plaintext"> /gene="gtrOC1"</span>
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<pre style="margin: 0;"> <span id="LC1450" class="line" lang="plaintext"> /codon_start=1</span>
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="plaintext"> /transl_table=11</span>
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<pre style="margin: 0;"> <span id="LC1452" class="line" lang="plaintext"> /product="GtrOC1 glycosyltransferase"</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1749,7 +1749,7 @@ FEATURES Location/Qualifiers</td>
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<pre style="margin: 0;"> <span id="LC1749" class="line" lang="plaintext"> /note="sequence from NCBI WGS accession number</span>
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="plaintext"> AMTB01000038 REGION: 221522..230586"</span>
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="plaintext"> CDS 1..888</span>
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<pre style="margin: 0;">-<span id="LC1752" class="line" lang="plaintext"> /gene="gtrOC1"<span class="idiff left right">"</span></span>
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="plaintext"> /gene="gtrOC1"</span>
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<pre style="margin: 0;"> <span id="LC1753" class="line" lang="plaintext"> /codon_start=1</span>
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<pre style="margin: 0;"> <span id="LC1754" class="line" lang="plaintext"> /transl_table=11</span>
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1755
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<pre style="margin: 0;"> <span id="LC1755" class="line" lang="plaintext"> /product="GtrOC1 glycosyltransferase"</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2038,7 +2038,7 @@ FEATURES Location/Qualifiers</td>
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2038
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<td class="diff-line-num new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2038
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<pre style="margin: 0;"> <span id="LC2038" class="line" lang="plaintext"> /note="sequence from NCBI WGS accession number</span>
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<td class="diff-line-num old_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2039
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<td class="diff-line-num new_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2039
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2039" class="line" lang="plaintext"> AMFY01000013 REGION: 222496..228777"</span>
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<td class="diff-line-num old_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2040
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<td class="diff-line-num new_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2040
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2040" class="line" lang="plaintext"> CDS 1..888</span>
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<td class="diff-line-num old old_line" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2041
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<td class="diff-line-num new_line old" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2041" class="line" lang="plaintext"> /gene="gtrOC1"<span class="idiff left right">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2041
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<pre style="margin: 0;">+<span id="LC2041" class="line" lang="plaintext"> /gene="gtrOC1"</span>
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<td class="diff-line-num old_line" data-linenumber="2042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2042
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<td class="diff-line-num new_line" data-linenumber="2042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2042
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2042" class="line" lang="plaintext"> /codon_start=1</span>
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<td class="diff-line-num old_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2043
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<td class="diff-line-num new_line" data-linenumber="2043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2043
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2043" class="line" lang="plaintext"> /transl_table=11</span>
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<td class="diff-line-num old_line" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2044
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<td class="diff-line-num new_line" data-linenumber="2044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2044
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2044" class="line" lang="plaintext"> /product="GtrOC1 glycosyltransferase"</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2245,7 +2245,7 @@ FEATURES Location/Qualifiers</td>
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<td class="diff-line-num old_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2245
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2245
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<pre style="margin: 0;"> <span id="LC2245" class="line" lang="plaintext"> /note="sequence from NCBI WGS accession number</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2246
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<td class="diff-line-num new_line" data-linenumber="2246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2246
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2246" class="line" lang="plaintext"> AMFI01000027 REGION: complement(34336..40843)"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2247
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<td class="diff-line-num new_line" data-linenumber="2247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2247
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2247" class="line" lang="plaintext"> CDS 1..888</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2248
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<pre style="margin: 0;">-<span id="LC2248" class="line" lang="plaintext"> /gene="gtrOC1"<span class="idiff left right">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="plaintext"> /gene="gtrOC1"</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2249
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2249
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2249" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2250
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<td class="diff-line-num new_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2250
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2250" class="line" lang="plaintext"> /transl_table=11</span>
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<td class="diff-line-num old_line" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2251
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2251
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<pre style="margin: 0;"> <span id="LC2251" class="line" lang="plaintext"> /product="GtrOC1 glycosyltransferase"</span>
</pre>
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