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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
| author | iuc |
|---|---|
| date | Thu, 23 Jun 2022 22:32:13 +0000 |
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><title>SynDivA Report</title><link href="http://twitter.github.com/bootstrap/assets/css/bootstrap.css" rel="stylesheet" /><style type="text/css">body {padding-top: 40px;}.subhead {padding: 40px 0;}.subhead h1 {font-size: 60px;}.fasta { font-family: Monaco, Menlo, Consolas, "Courier New", monospace; font-size: 12px;}code.grey{color: #636D71;}</style></head><body><a id="top"></a><div class="navbar navbar-fixed-top"><div class="navbar-inner"><div class="container"><a class="brand" href="#top">SynDivA Report</a><div class="nav-collapse collapse"><ul class="nav"><li><a href="#input">Input data</a></li><li><a href="#analysis">Sequences analysis</a></li><li><a href="#variable">Variable regions analysis</a></li><li><a href="#cluster">Clustering</a></li><li><a href="#stat">Statistics</a></li><li><a href="#annex">Annex</a></li></ul></div></div></div></div><div class="container-fluid"><header class="subhead"><h1>SynDivA Report</h1></header><div class="page-header"><a id="input"></a><h2>Input data</h2></div><p>Input file:<br/><code class="grey">syndiva_datatest.fasta</code></p><p>Number of sequences in input file:<br/><code class="grey">36</code></p><p>Pattern of the sequence bank:<br/><code class="grey">AAAGSSVSSVPTKLEVVAATPTSLLISWDA:4-6:V:1:YYRITYGETGGNSPVQEFTVPG:3:TATISGLSPGVDYTITVYA:11-12:PISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAETVESCLAKSHTENSFTNVWKDDKTLDRYANYE</code></p><p>5' restriction site:<br/><code class="grey">GCGGCCGC</code></p><p>3' restriction site:<br/><code class="grey">GGTACC</code></p><div class="page-header"><a id="analysis"></a><h2>Sequences analysis</h2></div><p>Caption:</p><ul><li class="text-success">Valid sequences that will be part of the next analysis </li><li class="text-warning">Good sequences but will not be part of the next analysis</li><li class="text-error">Rejected sequences</li></ul><table class="table table-striped table-bordered"><tr><th class="text-error">Absence of restriction sites</th><th class="text-error">Incorrect number of nucleotides between the restriction sites</th><th class="text-error">Stop codon <u>inside</u> the area of interest</th><th class="text-warning">Mutation in the conserved regions</th><th class="text-success">Valid sequences</th><th>Amber codon in the sequence (<u>inside</u> the area of interest)</th></tr><tr><td class="text-error">1 sequence(s) (2.78%)</td><td class="text-error">6 sequence(s) (16.67%)</td><td class="text-error">25 sequence(s) (69.44%)</td><td class="text-warning">0 sequence(s) (0.00%)</td><td class="text-success">4 sequence(s) (11.11%)</td><td>0 sequence(s)</td></tr><tr><td class="text-error">XL2-3_PSEXSEQ-REV_34</td><td class="text-error">XL1_22_PSEXSEQ-REV_24<br/>XL1_24_PSEXSEQ-REV_26<br/>XL1_30_PSEXSEQ-REV_30<br/>XL1_4_PSEXSEQ-REV_8<br/>XL2-2_PSEXSEQ-REV_33<br/>XL3-4_PSEXSEQ-REV_40</td><td class="text-error">XL1_10_PSEXSEQ-REV_13<br/>XL1_11_PSEXSEQ-REV_14<br/>XL1_13_PSEXSEQ-REV_16<br/>XL1_14_PSEXSEQ-REV_17<br/>XL1_15_PSEXSEQ-REV_18<br/>XL1_16_PSEXSEQ-REV_19<br/>XL1_17_PSEXSEQ-REV_20<br/>XL1_1_PSEXSEQ-REV_5<br/>XL1_23_PSEXSEQ-REV_25<br/>XL1_25_PSEXSEQ-REV_27<br/>XL1_26_PSEXSEQ-REV_28<br/>XL1_29_PSEXSEQ-REV_29<br/>XL1_33_PSEXSEQ-REV_23<br/>XL1_3_PSEXSEQ-REV_7<br/>XL1_5_PSEXSEQ-REV_9<br/>XL1_6_PSEXSEQ-REV_10<br/>XL1_8_PSEXSEQ-REV_11<br/>XL1_9_PSEXSEQ-REV_12<br/>XL2-1_PSEXSEQ-REV_32<br/>XL2-4_PSEXSEQ-REV_35<br/>XL2-5_PSEXSEQ-REV_36<br/>XL3-1_PSEXSEQ-REV_37<br/>XL3-2_PSEXSEQ-REV_38<br/>XL3-3_PSEXSEQ-REV_39<br/>XL3-5_PSEXSEQ-REV_41</td><td class="text-warning"></td><td class="text-success">XL1_12_PSEXSEQ-REV_15<br/>XL1_18_PSEXSEQ-REV_21<br/>XL1_19_PSEXSEQ-REV_22<br/>XL1_2_PSEXSEQ-REV_6</td><td></td></tr></table><div class="page-header"><a id="variable"></a><h2>Variable regions analysis</h2></div><p>The following group of sequences are identical clones on the variable regions:</p><p>No clone was found.</p><p>Here's the distribution of the repeated sequences in variable regions:</p><table class="table table-striped table-bordered"><thead><tr><th>Variable region</th><th>Repeated sequence</th><th>Number of occurrences (percentage of valid sequences)</th></tr></thead><tbody><tr><td rowspan="1">3</td><td>YSY</td><td>2 (50.00%)</td></tr></tbody></table><div class="page-header"><a id="cluster"></a><h2>Clustering</h2></div><p>The following clusters were generated by MCL:</p><div class="row-fluid"><div class="span6"><pre>4 sequences (100.00% of valid sequences)<br/>XL1_12_PSEXSEQ-REV_15<br/>XL1_18_PSEXSEQ-REV_21<br/>XL1_19_PSEXSEQ-REV_22<br/>XL1_2_PSEXSEQ-REV_6 </pre></div></div><div class="page-header"><a id="stat"></a><h2>Statistics</h2></div><p>Here's some statistics about the valid sequences:</p><p>Mean for the pairwise alignement scores: 20.01<br/>Standard deviation: 2.93</p><div class="row-fluid"><div class="span6"><img src="distri.png" alt="Distribution of the pairwise alignment score"></div><div class="span6"><table class="table table-striped table-bordered"><thead><tr><th>Pairwise Alignment Score</th><th>Number of occurrences</th></tr></thead><tbody><tr><td>16.67</td><td>1</td></tr><tr><td>17.24</td><td>1</td></tr><tr><td>19.23</td><td>1</td></tr><tr><td>19.35</td><td>1</td></tr><tr><td>22.58</td><td>1</td></tr><tr><td>25.00</td><td>1</td></tr></tbody></table></div></div><div class="page-header"><a id="annex"></a><h2>Annex</h2></div><p><strong>Valid protein sequences</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">>XL1_12_PSEXSEQ-REV_15 AAAGSSVSSVPTKLEVVAATPTSLLISWDANLPNSAVHYYRITYGETGGNSPVQEFTVPGSSYTATISGLSPGVDYTITV YAHNDCNTIVATCPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAR >XL1_18_PSEXSEQ-REV_21 AAAGSSVSSVPTKLEVVAATPTSLLISWDAIYRPVAYYRITYGETGGNSPVQEFTVPGYSYTATISGLSPGVDYTITVYA PIGHFDVLVTIPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRD >XL1_19_PSEXSEQ-REV_22 AAAGSSVSSVPTKLEVVAATPTSLLISWDASIFRGIVLYYRITYGETGGNSPVQEFTVPGYSYTATISGLSPGVDYTITV YAHGTSFSAISCAFPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAM >XL1_2_PSEXSEQ-REV_6 AAAGSSVSSVPTKLEVVAATPTSLLISWDAPLGDVFYYRITYGETGGNSPVQEFTVPGSYYTATISGLSPGVDYTITVYA TGARTSADGFIPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAR </textarea><p>Multiple sequence alignment of the <strong>valid sequences</strong> generated by Clustal Omega:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">CLUSTAL O(1.2.4) multiple sequence alignment XL1_12_PSEXSEQ-REV_15 AAAGSSVSSVPTKLEVVAATPTSLLISWDANLPNSAVHYYRITYGETGGNSPVQEFTVPG XL1_18_PSEXSEQ-REV_21 AAAGSSVSSVPTKLEVVAATPTSLLISWDAIY--RPVAYYRITYGETGGNSPVQEFTVPG XL1_19_PSEXSEQ-REV_22 AAAGSSVSSVPTKLEVVAATPTSLLISWDASIFRGIVLYYRITYGETGGNSPVQEFTVPG XL1_2_PSEXSEQ-REV_6 AAAGSSVSSVPTKLEVVAATPTSLLISWDAPL--GDVFYYRITYGETGGNSPVQEFTVPG ****************************** * ********************** XL1_12_PSEXSEQ-REV_15 SSYTATISGLSPGVDYTITVYAHNDCNTI-VATCPISINYRTGTGGSGGSHHHHHHHHGG XL1_18_PSEXSEQ-REV_21 YSYTATISGLSPGVDYTITVYAPIGHFDV-LVTIPISINYRTGTGGSGGSHHHHHHHHGG XL1_19_PSEXSEQ-REV_22 YSYTATISGLSPGVDYTITVYAHGTSFSAISCAFPISINYRTGTGGSGGSHHHHHHHHGG XL1_2_PSEXSEQ-REV_6 SYYTATISGLSPGVDYTITVYATGARTSA-DGFIPISINYRTGTGGSGGSHHHHHHHHGG ******************** ************************** XL1_12_PSEXSEQ-REV_15 SYPYDVPDYAPRVG*GRVGSKDIRAR XL1_18_PSEXSEQ-REV_21 SYPYDVPDYAPRVG*GRVGSKDIRD- XL1_19_PSEXSEQ-REV_22 SYPYDVPDYAPRVG*GRVGSKDIRAM XL1_2_PSEXSEQ-REV_6 SYPYDVPDYAPRVG*GRVGSKDIRAR ************************ </textarea><p><strong>Protein sequences with an incorrect number of nucleotides between the restriction sites</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">>XL1_22_PSEXSEQ-REV_24 AAAGSSVSSVPTKLEVVAATPTSLLISWDALITFVAYYRITYGETGGTPRFRNSPSRVLILPQRFPACHRVSTIPLRFTL PTPPTTTTSSSRFLSITVPVPAVRAVAITITITIMVVRIRMTCQTMHHAWARDAWDPKISEPI >XL1_24_PSEXSEQ-REV_26 AAAGSSVSSVPTKLEVVAATPTSLLISWDAHSSPDYVCYYRITYGETGVTPGSGIHRPG*FLNRNDFRPVTGCRLYHYGL RFELLTYLLIEL*SDFYQLPYRYRRFGR*PSPSPSPSWWFVSV*RARLCTTRGLGTRGIQRYQSK >XL1_30_PSEXSEQ-REV_30 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPSAATPTTRFL SITVPVPAVRAVAITITITIMVVRIRMTCQTMHHAWARDAWDPKIS >XL1_4_PSEXSEQ-REV_8 AAAGSSVSSVPTKLEVVAATPTSLLISWDAPFTDHCVVYYRITYGETGGNPRFRNSPSRVLIIPQRFPACHRVSTIPLRF TLTTPAATTTAPTPRFLSITVPVPAVRAVAITITITIMVVRIRMTCQTMHHAWARDAWDPKISEQS >XL2-2_PSEXSEQ-REV_33 AAAGSSVSSVPTKLEVVAATPTSLLISWDACHTFVNYYRITYGETGGNSPVQEFTRPGLFLYRNDFRPVTGCRLYHYGLR *PLPPLLRLPRPDFYQLPYRYRRFGR*PSPSPSPSWWFVSV*RARLCTTRGLGTRGIQRYPE >XL3-4_PSEXSEQ-REV_40 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTSRVLIIPQRFPACHRVSTIPLRFTL PASTTASSTAADFYQLPYRYRRFGR*PSPSPSPSWWFVSV*RARLCTTRGLGTRGIQRYQSER </textarea><p><strong>Protein sequences with a stop codon</strong> in FASTA format:</p><textarea class="span8 fasta" type="text" rows="20" readonly="readonly">>XL1_10_PSEXSEQ-REV_13 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAT >XL1_11_PSEXSEQ-REV_14 AAAGSSVSSVPTKLEVVAATPTSLLISWDAHGNCVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAE >XL1_13_PSEXSEQ-REV_16 AAAGSSVSSVPTKLEVVAATPTSLLISWDAPRSFVRYYRITYGETGGNSPVQEFTVPGSYSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAK >XL1_14_PSEXSEQ-REV_17 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSYTATISGLSPGVDYTITVYA RYFIYSYISHSTPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAK >XL1_15_PSEXSEQ-REV_18 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRC >XL1_16_PSEXSEQ-REV_19 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGYYSTATISGLSPGVDYTITVYA CGGVNANSSDCFPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAK >XL1_17_PSEXSEQ-REV_20 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SVPIHFSCRGCPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIS >XL1_1_PSEXSEQ-REV_5 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIP >XL1_23_PSEXSEQ-REV_25 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSYYTATISGLSPGVDYTITVYA GDISDNPFSRCPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAN >XL1_25_PSEXSEQ-REV_27 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAR >XL1_26_PSEXSEQ-REV_28 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKRYP >XL1_29_PSEXSEQ-REV_29 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAP >XL1_33_PSEXSEQ-REV_23 AAAGSSVSSVPTKLEVVAATPTSLLISWDASQSNVSYYRITYGETGGNSPVQEFTVPGCYSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAEN >XL1_3_PSEXSEQ-REV_7 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAS >XL1_5_PSEXSEQ-REV_9 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAN >XL1_6_PSEXSEQ-REV_10 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGYYSTATISGLSPGVDYTITVYA NATVSNFHPINSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDFRAK >XL1_8_PSEXSEQ-REV_11 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAK >XL1_9_PSEXSEQ-REV_12 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVCYYRITYGETGGNSPVQEFTVPGSYSTATISGLSPGVDYTITVYA SLVNDDVHAVHHPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIQS >XL2-1_PSEXSEQ-REV_32 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKEIRAM >XL2-4_PSEXSEQ-REV_35 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAN >XL2-5_PSEXSEQ-REV_36 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSYYTATISGLSPGVDYTITVYA SGYCVIVANSYPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIP >XL3-1_PSEXSEQ-REV_37 AAAGSSVSSVPTKLEVVAATPTSLLISCDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRSR >XL3-2_PSEXSEQ-REV_38 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAR >XL3-3_PSEXSEQ-REV_39 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAS >XL3-5_PSEXSEQ-REV_41 AAAGSSVSSVPTKLEVVAATPTSLLISWDAS*SSVSYYRITYGETGGNSPVQEFTVPGSSSTATISGLSPGVDYTITVYA SSS*RISSSSSSPISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAT </textarea></div></body></html>