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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/blends-team/med/commit/15637de9ba6d7cf6d4fba6946661901904e66ac9">15637de9</a></strong>
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<span>by Steffen Möller</span>
<i>at 2018-05-03T14:37:09+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">"fasta" (name in Bio-Linux) was just uploaded to new as "fasta3".</pre>
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<h4>1 changed file:</h4>
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<a href="#26b0fba1305554e48a6078ef69d0cfe948ad5765">
tasks/bio
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<h4>Changes:</h4>
<li id="26b0fba1305554e48a6078ef69d0cfe948ad5765">
<a href="https://salsa.debian.org/blends-team/med/commit/15637de9ba6d7cf6d4fba6946661901904e66ac9#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2086" 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">@@ -2086,27 +2086,6 @@ Pkg-Description: detect coding regions in DNA sequences, even if of low quality</td>
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<pre style="margin: 0;"> <span id="LC2086" class="line" lang="mosel"><span class="s1" style="color: #d14;"> EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.</span></span>
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<pre style="margin: 0;"> <span id="LC2087" class="line" lang="mosel"><span class="s1" style="color: #d14;">Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2088" class="line" lang="mosel"></span>
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2089
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: fasta</span></span>
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<pre style="margin: 0;">-<span id="LC2090" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://www.ebi.ac.uk/Tools/fasta/</span></span>
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<pre style="margin: 0;">-<span id="LC2091" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: no inclusion into commercial product</span></span>
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<pre style="margin: 0;">-<span id="LC2092" class="line" lang="mosel"><span class="s1" style="color: #d14;">Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk></span></span>
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<pre style="margin: 0;">-<span id="LC2093" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/</span></span>
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: searching DNA and protein databases</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2095" 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="LC2095" class="line" lang="mosel"><span class="s1" style="color: #d14;"> FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact</span></span>
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<pre style="margin: 0;">-<span id="LC2096" class="line" lang="mosel"><span class="s1" style="color: #d14;"> that it can be used for a fast protein comparison or a fast</span></span>
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<pre style="margin: 0;">-<span id="LC2097" class="line" lang="mosel"><span class="s1" style="color: #d14;"> nucleotide comparison. This program achieves a high level of</span></span>
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="mosel"><span class="s1" style="color: #d14;"> sensitivity for similarity searching at high speed. This is achieved</span></span>
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="mosel"><span class="s1" style="color: #d14;"> by performing optimised searches for local alignments using a</span></span>
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<pre style="margin: 0;">-<span id="LC2100" class="line" lang="mosel"><span class="s1" style="color: #d14;"> substitution matrix. The high speed of this program is achieved by</span></span>
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="mosel"><span class="s1" style="color: #d14;"> using the observed pattern of word hits to identify potential matches</span></span>
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<pre style="margin: 0;">-<span id="LC2102" class="line" lang="mosel"><span class="s1" style="color: #d14;"> before attempting the more time consuming optimised search. The</span></span>
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<pre style="margin: 0;">-<span id="LC2103" class="line" lang="mosel"><span class="s1" style="color: #d14;"> trade-off between speed and sensitivity is controlled by the ktup</span></span>
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<pre style="margin: 0;">-<span id="LC2104" class="line" lang="mosel"><span class="s1" style="color: #d14;"> parameter, which specifies the size of the word. Increasing the ktup</span></span>
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<pre style="margin: 0;">-<span id="LC2105" class="line" lang="mosel"><span class="s1" style="color: #d14;"> decreases the number of background hits. Not every word hit is</span></span>
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<pre style="margin: 0;">-<span id="LC2106" class="line" lang="mosel"><span class="s1" style="color: #d14;"> investigated but instead initially looks for segment'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">containing</span></span>
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<td class="diff-line-num new_line old" data-linenumber="2089" 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="LC2107" class="line" lang="mosel"> <span class="n" style="color: #333;">several</span> <span class="n" style="color: #333;">nearby</span> <span class="n" style="color: #333;">hits</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2108" 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">
2108
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<td class="diff-line-num new_line old" data-linenumber="2089" 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="LC2108" class="line" lang="mosel"><span class="n" style="color: #333;">Remark</span><span class="p">:</span> <span class="n" style="color: #333;">This</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">ships</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">BioLinux</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">envgen</span><span class="p">.</span><span class="n" style="color: #333;">nox</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">uk</span><span class="p">/</span><span class="n" style="color: #333;">biolinux</span><span class="p">.</span><span class="n" style="color: #333;">html</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2109" 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">
2109
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<pre style="margin: 0;">-<span id="LC2109" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="2110" 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">
2110
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2089
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<pre style="margin: 0;"> <span id="LC2089" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: lamarc</span></span>
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<td class="diff-line-num old_line" data-linenumber="2111" 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">
2111
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<td class="diff-line-num new_line" data-linenumber="2090" 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">
2090
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<pre style="margin: 0;"> <span id="LC2090" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/</span></span>
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<td class="diff-line-num old_line" data-linenumber="2112" 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">
2112
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<td class="diff-line-num new_line" data-linenumber="2091" 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">
2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="mosel"><span class="s1" style="color: #d14;">Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html</span></span>
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