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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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<strong><a href="https://salsa.debian.org/blends-team/med/commit/a0e78e1d4f35f6e14ab18eeceb854602263cb991">a0e78e1d</a></strong>
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<span>by Steffen Möller</span>
<i>at 2018-05-31T22:57:19+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update bio - uploaded ESTScan to new</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/a0e78e1d4f35f6e14ab18eeceb854602263cb991#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</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">@@ -2067,39 +2067,6 @@ Pkg-Description: processes, clusters and annotates EST data</td>
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="mosel"><span class="s1" style="color: #d14;"> a MySQL database or web-browsable search tool.</span></span>
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<pre style="margin: 0;"> <span id="LC2068" 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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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC2070" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: estscan</span></span>
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<pre style="margin: 0;">-<span id="LC2071" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://estscan.sourceforge.net/</span></span>
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<pre style="margin: 0;">-<span id="LC2072" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: free</span></span>
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<pre style="margin: 0;">-<span id="LC2073" class="line" lang="mosel"><span class="s1" style="color: #d14;">Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk></span></span>
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<pre style="margin: 0;">-<span id="LC2074" 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="LC2075" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: detect coding regions in DNA sequences, even if of low quality</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2076" 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="LC2076" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ESTScan is a program that can detect coding regions in DNA sequences,</span></span>
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<pre style="margin: 0;">-<span id="LC2077" class="line" lang="mosel"><span class="s1" style="color: #d14;"> even if they are of low quality. It will also detect and correct</span></span>
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<pre style="margin: 0;">-<span id="LC2078" class="line" lang="mosel"><span class="s1" style="color: #d14;"> sequencing errors that lead to fr ameshifts.</span></span>
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<pre style="margin: 0;">-<span id="LC2079" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<pre style="margin: 0;">-<span id="LC2080" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ESTScan is not a gene prediction program, nor is it an open reading</span></span>
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<pre style="margin: 0;">-<span id="LC2081" class="line" lang="mosel"><span class="s1" style="color: #d14;"> frame detector. In fact, its strength lies in the fact that it does</span></span>
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<pre style="margin: 0;">-<span id="LC2082" class="line" lang="mosel"><span class="s1" style="color: #d14;"> not require an open reading frame to detect a coding region. As a</span></span>
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<pre style="margin: 0;">-<span id="LC2083" class="line" lang="mosel"><span class="s1" style="color: #d14;"> result, the program may miss a few translated amino acids at either</span></span>
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<pre style="margin: 0;">-<span id="LC2084" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the N or the C terminus, but will detect coding regions with high</span></span>
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<pre style="margin: 0;">-<span id="LC2085" class="line" lang="mosel"><span class="s1" style="color: #d14;"> selectivity and sensitivity.</span></span>
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<pre style="margin: 0;">-<span id="LC2086" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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<pre style="margin: 0;">-<span id="LC2087" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Similarly to GENSCAN, ESTScan uses a Markov model to represent the</span></span>
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<pre style="margin: 0;">-<span id="LC2088" class="line" lang="mosel"><span class="s1" style="color: #d14;"> bias in hexanucleotide usage found in coding regions relative to</span></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;"> non-coding regions. Additionally, ESTScan allows insertions and</span></span>
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2090
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<pre style="margin: 0;">-<span id="LC2090" class="line" lang="mosel"><span class="s1" style="color: #d14;"> deletions when these improve the coding region statistics. Further</span></span>
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2091
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<pre style="margin: 0;">-<span id="LC2091" class="line" lang="mosel"><span class="s1" style="color: #d14;"> details can be found at:</span></span>
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2092
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<pre style="margin: 0;">-<span id="LC2092" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://www.ch.embnet.org/software/ESTScan2_help.html</span></span>
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2093
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<pre style="margin: 0;">-<span id="LC2093" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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2094
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="mosel"><span class="s1" style="color: #d14;"> References:</span></span>
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2095
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<pre style="margin: 0;">-<span id="LC2095" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing</span></span>
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2096
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<pre style="margin: 0;">-<span id="LC2096" class="line" lang="mosel"><span class="s1" style="color: #d14;"> errors by combining Hidden Markov models Bioinformatics 19,</span></span>
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2097
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<pre style="margin: 0;">-<span id="LC2097" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ii103-ii112.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2098" 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">
2098
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<pre style="margin: 0;">-<span id="LC2098" class="line" lang="mosel"><span class="s1" style="color: #d14;"> * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for</span></span>
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2099
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<pre style="margin: 0;">-<span id="LC2099" class="line" lang="mosel"><span class="s1" style="color: #d14;"> detecting, evaluating, and reconstructing potential coding regions in</span></span>
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2100
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<pre style="margin: 0;">-<span id="LC2100" 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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2101
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<pre style="margin: 0;">-<span id="LC2101" 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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2102
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<pre style="margin: 0;">-<span id="LC2102" class="line" lang="mosel"></span>
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2103
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2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: lamarc</span></span>
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2104
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2071
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<pre style="margin: 0;"> <span id="LC2071" 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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2105
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2072
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<pre style="margin: 0;"> <span id="LC2072" 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 match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2412,6 +2379,9 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html</td>
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2412
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2379
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<pre style="margin: 0;"> <span id="LC2379" class="line" lang="mosel"></span>
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2413
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2380
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<pre style="margin: 0;"> <span id="LC2380" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">trace2dbest</span></span>
</pre>
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2414
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2381
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<pre style="margin: 0;"> <span id="LC2381" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="2382" 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">
2382
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<pre style="margin: 0;">+<span id="LC2382" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">estscan</span></span>
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2383
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<pre style="margin: 0;">+<span id="LC2383" 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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2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="mosel"></span>
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2415
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<td class="diff-line-num new_line" data-linenumber="2385" 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">
2385
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<pre style="margin: 0;"> <span id="LC2385" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">profit</span></span>
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2416
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2386
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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="mosel"><span class="n" style="color: #333;">WNPP</span><span class="p">:</span> <span class="m" style="color: #099;">525428</span></span>
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<td class="diff-line-num old_line" data-linenumber="2417" 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">
2417
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<td class="diff-line-num new_line" data-linenumber="2387" 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">
2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="mosel"><span class="n" style="color: #333;">Remark</span><span class="p">:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">authors</span> <span class="n" style="color: #333;">need</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">change</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">license</span><span class="p">,</span> <span class="n" style="color: #333;">still</span><span class="p">.</span></span>
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