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‎doc/Release.html‎

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<a id=top>
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<!--#include virtual="./ssi/start1.html" -->
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<h4>v3.3.1 1-Sept-2021</h4>
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The singleTCW database has a small schema update that will be applied the first time an existing
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database is viewed.
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<p><ttp>runSingleTCW</ttp> -- Annotate
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<ul>
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<li>sTCWdb version sdb6.0: The percent similarity (identity) is stored as a real number instead of an integer.
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<li><font color=green>NEW</font> Prune Hits - there are many hits with the exact same coordinates and/or descriptions.
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A new function removes all but the best based on same alignment values or same description.
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This function can be set to run in the AnnoDBs <ttl>Options</ttl> or from the command line.
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<li>Tiny changes;
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<ul>
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<li>DIAMOND - removed '--max-hsps 1' as TCW defaults because it is a DIAMOND default.
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Removed '--top 20' as this misses some good descriptions.
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<li>TCW was only loading 25 hits per annoDB. This restriction has been removed since the user
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can set the limit in the search programs parameters.
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<li>This really isn't a problem, but I fixed it any way as it could be confusing: If there were multiple hits with the
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same bit_score and E-value, it was using the one with the highest rank for the "Best Bit" assignment,
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which was changed to lowest.
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<li>Tiny bug fix in Multi-Frame: If a sequence had an NT hit, it was typically incorrectly marked as 'Multi-frame'.
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</ul>
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</ul>
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<ttp>viewSingleTCW</ttp> - tiny adjustments
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<ul>
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<li>Sequence Detail:
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<ul>
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<li>A new <ttl>Show</ttl> button shows all columns for a selected hit (the Hit Table
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only provides a subset of all columns).
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<li>The Hit Table now sorts on bit-score, e-value, %sim in that order (the addition of %sim is new).
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</ul>
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<li>Basic Hit:
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<ul>
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<li>The Bit-score has been added to the columns.
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<li>DE values of "-" will sort to the bottom of the table.
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</ul>
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<li>A reading frame was being assigned to an NT hit -- it now has a value of "-".
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<li>Tiny bug fix in alignments: In rare instance, aligning an NT-NT following by a NT-AA could create a bogus NT-AA alignment.
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</ul>
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<ttp>viewMultiTCW</ttp>
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<ul>
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<li>Sequence Table: DE values of "-" will sort to the bottom of the table and the sort will ignore
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the minus sign before an DE value (as <ttp>viewSingleTCW</ttp> does).
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</ul>
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<ttl>Software details</ttl>
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<ul>
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<li>The Best Bits, etc assignment was moved from DoUniProt.java to DoUniAssign.java
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</ul>
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<!-------------------------------------------------------------------->
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<h4>v3.3.0 15-August-2021</h4>
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<i>Update existing multiTCW databases for this release</i>:
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There is a small mTCWdb schema change, which will be updated the first time you access the database. However,
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on a selected DE p-value, it will overwrite an existing column.
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<li>The DE and GO p-value columns will be displayed in <ttp>viewSingleTCW</ttp> in the order that
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the DE p-value columns are created (only guaranteed if created with v3.2.6 or later).
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<li>The online <a href=stcw/DiffExp.html>DE User Manual</a> was significantly updated.
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<li>The online <a href="stcw/DiffExp.html">DE User Manual</a> was significantly updated.
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</ul>
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<ttp>runSingleTCW</ttp> - <b>Overview</b>

‎doc/Summary.html‎

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</ul>
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<a id=task></a>
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<h2>Programs</h2>
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<a href="img/bullet2.gif"><img src="img/bullet2.gif" alt="bullet" style="border: 0px; width: 20px"></a>
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<img src="img/bullet2.gif" alt="bullet" style="border: 0px; width: 20px">
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<i><u>singleTCW contains four major programs:</u></i>
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<table class="tablex">
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<tr>
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<td class="top"><a href="./tour/viewSingle/img/mainTable.png"><img src="./tour/viewSingle/img/mainTable.png" alt="" style="border: 1px solid black; width: 100px"></a>
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</table>
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<a href="img/bullet2.gif"><img src="img/bullet2.gif" alt="bullet" style="border: 0px; width: 20px"></a>
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<img src="img/bullet2.gif" alt="bullet" style="border: 0px; width: 20px">
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<i><u>multiTCW contains two major programs</u></i>:
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<table class="tablex">
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<tr><td class="top">

‎doc/index.html‎

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<tr> <td colspan=3>&nbsp;&nbsp;
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<tr><td colspan=3> Details</td></tr>
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<tr> <td>&nbsp;&nbsp;<td><a href="stcw/AnnoGuide.html">Updating annotation</a></td>
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<td>Removing, adding, updating annotation</td></tr>
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<tr> <td>&nbsp;&nbsp;<td><a href="stcw/AnnoGuide.html">Annotate Details</a></td>
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<td>Removing, adding, updating annotation; pruning hits</td></tr>
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<tr> <td>&nbsp;&nbsp;<td><a href="stcw/ORF.html">ORF finder</a></td>
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<td>Description of options, algorithm, outputs, and results. </td></tr>
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<tr> <td>&nbsp;&nbsp;<td><a href="stcw/AssemGuide.html">Assembly Details</a></td>

‎doc/ov/sDemo.html‎

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<h2>TCW overview for tra </h2>
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<table width=700 border=1><tr><td>
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<pre>
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Project: tra #Seqs: 211 #Hits: 9,584 #GOs: 5,294 TPM Seq-DE GO-Enrich Pairs
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Project: tra #Seqs: 211 #Hits: 12,267 #GOs: 6,651 TPM Seq-DE GO-Enrich Pairs
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12-Aug-21 Build Database sequences loaded from external source
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12-Aug-21 Last Annotation with sTCW v3.3.0
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26-Aug-21 Build Database sequences loaded from external source
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26-Aug-21 Last Annotation with sTCW v3.3.1
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INPUT
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Counts:
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ANNOTATIONS
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Hit Statistics:
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Sequences with hits 210 (99.5%) Bases covered by hit 180,729 (79.4%)
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Unique hits 9,584 Total bases 227,683
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Total sequence hits 13,224
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Sequences with hits 210 (99.5%) Bases covered by hit 180,582 (79.3%)
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Unique hits 12,267 Total bases 227,683
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Total sequence hits 18,013
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annoDBs (Annotation databases): 8 (see Legend below)
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annoDBs (Annotation databases): 7 (see Legend below)
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ANNODB ONLY BITS ANNO UNIQUE TOTAL AVG Rank HAS (%Seqs) AVG COVER COVER
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%SIM =1 HIT %SIM >=50 >=90
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SP-plants 0 0 0 781 1,311 65.3 | 193 (91.5%) 70.1 62.7% 3.6%
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SP-invertebrates 0 0 1 329 590 48.3 | 126 (59.7%) 47.6 30.2% 0.8%
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SP-fungi 0 0 0 640 1,067 46.7 | 118 (55.9%) 47.0 27.1% 0.8%
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SP-bacteria 0 0 0 659 944 44.9 | 63 (29.9%) 45.8 25.4% 0%
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SP-fullSubset 0 0 0 757 1,515 48.7 | 137 (64.9%) 48.7 33.6% 0.7%
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TR-plants 7 207 207 4,122 4,858 77.4 | 210 (99.5%) 81.8 68.6% 8.6%
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TR-invertebrates 0 3 2 2,165 2,701 52.3 | 179 (84.8%) 54.5 39.7% 2.8%
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TF-PlantTFDB 0 0 0 131 238 47.0 | 123 (58.3%) 51.2 7.3% 0%
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Top 15 species from total: 1,312
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SP-plants 0 0 0 1,320 2,956 53.2 | 193 (91.5%) 69.6 61.1% 3.1%
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SP-invertebrates 0 0 0 610 1,252 42.0 | 126 (59.7%) 47.0 29.4% 0.8%
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SP-fungi 0 0 0 850 1,459 42.9 | 118 (55.9%) 46.4 24.6% 0.8%
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SP-bacteria 0 0 0 786 1,121 43.7 | 63 (29.9%) 45.4 25.4% 0%
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SP-fullSubset 0 0 0 1,261 2,291 44.2 | 137 (64.9%) 48.1 32.1% 0.7%
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TR-plants 9 207 207 4,535 5,217 75.5 | 210 (99.5%) 81.4 68.6% 8.6%
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TR-invertebrates 0 3 3 2,905 3,717 49.5 | 179 (84.8%) 54.0 39.1% 2.2%
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Top 15 species from total: 1,508
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SPECIES (25 char) BITS ANNO TOTAL SPECIES BITS ANNO TOTAL
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Musa acuminata 73 53 325 Anthurium amnicola 2 4 93
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Musa balbisiana 62 45 312 Vitis vinifera 2 3 91
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Ensete ventricosum 19 14 199 Dendrobium catenatum 2 2 63
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Elaeis guineensis 10 24 344 Macleaya cordata 2 2 43
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Phoenix dactylifera 9 19 319 Nelumbo nucifera 1 3 95
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Zingiber officinale 7 7 24 Apostasia shenzhenica 1 2 59
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Ananas comosus 4 11 432 Ricinus communis 1 2 31
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Meloidogyne enterolobii 3 0 9 Other 12 19 10,785
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Musa acuminata 75 54 325 Anthurium amnicola 2 4 101
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Musa balbisiana 59 42 313 Vitis vinifera 2 3 89
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Ensete ventricosum 19 14 214 Apostasia shenzhenica 2 3 67
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Elaeis guineensis 10 24 347 Dendrobium catenatum 2 2 73
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Phoenix dactylifera 9 19 318 Macleaya cordata 2 2 41
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Zingiber officinale 7 7 27 Nelumbo nucifera 1 3 95
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Ananas comosus 4 11 458 Ricinus communis 1 2 43
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Meloidogyne enterolobii 3 0 10 Other 12 20 15,492
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Gene Ontology Statistics:
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Unique GOs 5,294 Unique hits with GOs 8,124 (84.8%)
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Sequences with GOs 208 (98.6%) Seq best hit has GOs 194 (91.9%)
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Has goslim_plant 95
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biological_process 3,858 (72.9%) is_a 8,481
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molecular_function 821 (15.5%) part_of 898
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cellular_component 615 (11.6%)
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Unique GOs 6,651 Unique hits with GOs 10,670 (87.0%)
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Sequences with GOs 208 (98.6%) Seq best hit has GOs 194 (91.9%)
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Has goslim_plant 95
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biological_process 4,879 (73.4%) is_a 10,776
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molecular_function 1,026 (15.4%) part_of 1,176
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cellular_component 746 (11.2%)
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EXPRESSION
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TPM: (% of 211)
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RoOl 1(<1%) 16 (8%) 37(18%) 74(35%) 110(52%)
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StOl 0 (0%) 2 (1%) 12 (6%) 65(31%) 101(48%)
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Gene ontology enrichment: (% of 5,294)
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Gene ontology enrichment: (% of 6,651)
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<1E-5 <1E-4 <0.001 <0.01 <0.05
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RoSt 0 (0%) 1(<1%) 3(<1%) 54 (1%) 289 (5%)
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RoOl 0 (0%) 0 (0%) 3(<1%) 20(<1%) 187 (4%)
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StOl 0 (0%) 0 (0%) 0 (0%) 0 (0%) 36 (1%)
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RoSt 0 (0%) 0 (0%) 1(<1%) 51 (1%) 309 (5%)
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RoOl 0 (0%) 0 (0%) 2(<1%) 22(<1%) 166 (2%)
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StOl 0 (0%) 0 (0%) 0 (0%) 1(<1%) 48 (1%)
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SEQUENCES
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Sequence lengths:
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Pos2 13.7% %GC 43.71 48.80 36.27 Length 21k 182k 25k
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Pos3 16.6% CpG-O/E 0.87 0.71 0.63 AvgLen 101.2 860.8 117.1
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Similar pairs: 434
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Nucleotide 20
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Translated nucleotide 415
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Translated ORFs 369
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Similar pairs: 20
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Nucleotide 20
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LOCATIONS
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Sequences with location: 12 unique locations: 12
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-------------------------------------------------------------------
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PROCESSING INFORMATION:
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AnnoDB Files:
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Type Taxo FILE DB DATE ADD DATE EXECUTE
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sp plants uniprot_sprot_plants.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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sp invertebrates uniprot_sprot_invertebrates.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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sp fungi uniprot_sprot_fungi.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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sp bacteria uniprot_sprot_bacteria.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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sp fullSubset uniprot_sprot_fullSubset.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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tr plants uniprot_trembl_plants.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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tr invertebrates uniprot_trembl_invertebrates.fasta 27-Jan-21 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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tf PlantTFDB PlantTFDB_TCW.fa 25-Oct-20 12-Aug-21 diamond --max-hsps 1 --masking 0 --top 20
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Gene Ontology: go-basic.obo-Feb2021 GOdb: go_demo [GOs added with sTCW v3.3.0]
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Type Taxo FILE DB DATE ADD DATE EXECUTE
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sp plants uniprot_sprot_plants.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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sp invertebrates uniprot_sprot_invertebrates.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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sp fungi uniprot_sprot_fungi.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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sp bacteria uniprot_sprot_bacteria.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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sp fullSubset uniprot_sprot_fullSubset.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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tr plants uniprot_trembl_plants.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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tr invertebrates uniprot_trembl_invertebrates.fasta 27-Jan-21 26-Aug-21 diamond --masking 0
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Gene Ontology: go-basic.obo-Feb2021 GOdb: go_demo [GOs added with sTCW v3.3.1]
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GO Slim: goslim_plant
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ORF finder:

‎doc/stcw/AnnoDBs.html‎

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<!DOCTYPE html>
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<html>
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<!--#set var=TITLE value="Annotation Setup" -->
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<!--#set var=TITLE value="Annotation Setup and runAS" -->
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<!--#include virtual="../ssi/head.html" -->
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<body onload="init('set')">
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<a id="top"></a>

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