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v4.0.3
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‎docs/Release.html‎

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There have been many improvements, but the following provides some recent critical points.
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<font size="2">
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<table>
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<tr><td><a href="#v400">v4.0.2</a><td>7-July-22<td><ttp>Online help<td>Install at csoderlund.github.io/tcw
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<tr><td><a href="#v403">v4.0.3</a><td>14-July-22<td><ttp>All<td>Small improvements.
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<tr><td><a href="#v339">v3.3.9</a><td>27-Dec-21<td><ttp><ttp>runAS</ttp></ttp><td>Improved interface for full subset UniProt; updated Demo.
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<tr><td><a href="#v335">v3.3.5</a><td>04-Nov-21<td><ttp>viewSingle</ttp><td>log2FC TPM analysis
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<tr><td><a href="#v334">v3.3.4</a><td>18-Oct-21<td><ttp>runSingle</ttp><td><ttl>ORF finder</ttl> improvements
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</table>
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</font>
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<a id=v400></a>
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<a id=v403></a>
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<h4>v4.0.3 14-July-2022</h4>
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<ttp>runDE</ttp>
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<ul>
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<li>The <ttc>Close</ttc> and <ttc>Exit</ttc> did not work quite right in either the
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<ttp>runDE Database Chooser</ttp> or <ttp>runDE</ttp> window.
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These have been tidied up with additional Help added.
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</ul>
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<ttp>runSingleTCW</ttp>
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<ul>
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<li>ORF finder:
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<ol>
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<li>Really tiny bug: Very occasionally, it was assigning ORF=Hit remark incorrectly when ORF=Hit-3 and
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there was one AA at the end instead of stop codon (e.g. demoTra, tra_005).
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</ol>
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</ul>
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<ttp>viewSingleTCW</ttp>
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<ul>
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<li>Seq-Hit align:
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<ol>
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<li>The hit-ORF overlaps are highlighted in aquamarine (this happens when there is a stop codon in the hit region).
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<li>Really tiny bug: The 3'UTR was starting one early sometimes.
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</ol>
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</ul>
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<a id=v402></a>
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<h4>v4.0.2 7-July-2022</h4>
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Most documentation is in the TCW desktop applications except for the extensive
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documentation for building a single or comparative TCW database, which has
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BioRxiv publication
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</ul>
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<a id=v343></a>
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<a id=v400></a>
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<h4>v4.0.0 22-Mar-2022</h4>
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<p>General

‎docs/index.html‎

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TCW uses Java, mySQL, optionally R, and various <a href="./External.html">External</a> packages.
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It has been tested on Linux and Mac.
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<ul>
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<li>Last release: TCW v4.0.2 (7-July-22). See <a href="./Release.html">Release Notes</a>.
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<li>Last release: TCW v4.0.3 (14-July-22). See <a href="./Release.html">Release Notes</a>.
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Published in <a href="https://doi.org/10.1101/733311" class="ext" target="_blank">BioRxiv</a> (02-May-2022).
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‎docs/ov/mDemo.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>mTCW_ex overview</title>
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</head>
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<body>
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<center>
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<html><head><title>mTCW_ex overview</title></head><body><center>
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<h2>mTCW overview for ex</h2>
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<table style="border: 1px solid black; border-spacing: 0px; border-collapse: collapse; width=600">
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<tr><td>
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<pre>Project: ex Cluster: 1.0k Pairs: 846 Seqs: 707 Hits: 4.0k GOs: 8.0k PCC Stats KaKs Multi
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<table width=600 border=1><tr><td><pre>Project: ex Cluster: 1.0k Pairs: 846 Seqs: 707 Hits: 2.2k PCC Stats KaKs Multi
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Created: 21-Mar-22 v4.0.0 Last Update: 04-Apr-22 v4.0.1
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Created: 13-Jul-22 v4.0.3
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DATASETS: 3
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Type #Seq #annotated #annoDB Created Remark
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bar NT 250 250 3 15-Mar-22 exBar
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fly NT 207 207 3 15-Mar-22 exFly
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foo NT 250 250 3 15-Mar-22 exFoo
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bar NT 250 250 3 06-Jul-22 exBar
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fly NT 207 207 3 06-Jul-22 exFly
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foo NT 250 250 3 06-Jul-22 exFoo
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CLUSTER SETS: 5
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Statistics
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Prefix Method conLen sdLen Score1 SD Score2 SD
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CL Closure 579.75 58.50 3.72 1.06 0.78 0.15
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OM orthoMCL.OM-4 606.38 85.26 3.30 1.40 0.75 0.16
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B12 BBH bar,fly 540.22 62.63 3.58 1.10 0.72 0.18
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B13 BBH bar,foo 558.75 34.11 4.09 0.82 0.79 0.15
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CL Closure 579.80 58.52 3.72 1.06 0.78 0.15
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OM orthoMCL.OM-4 606.33 85.28 3.30 1.40 0.75 0.16
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B12 BBH bar,fly 540.34 62.71 3.58 1.10 0.72 0.18
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B13 BBH bar,foo 558.76 34.07 4.09 0.83 0.79 0.15
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B23 BBH fly,foo 559.57 70.82 3.98 1.28 0.80 0.21
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Sizes
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Prefix =2 =3 4-5 6-10 11-15 16-20 21-25 >25 Total #Seqs
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Prefix =2 =3 4-5 6-10 11-15 16-20 21-25 &gt;25 Total #Seqs
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CL 93 150 1 1 0 0 0 0 245 91.5%
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OM 50 186 3 3 0 0 0 0 242 98.0%
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B12 157 0 0 0 0 0 0 0 157 44.4%
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Pos1 Pos2 Pos3 Total GC CpG-Nt CpG-Cd
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Transition 9.3% 5.1% 35.0% 49.4% Both 38.0% 3.9% 2.2%
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Transversion 12.1% 8.2% 30.2% 50.6% Either 54.6% 11.4% 5.8%
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Transversion 12.1% 8.3% 30.3% 50.6% Either 54.6% 11.4% 5.8%
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ts/tv 0.77 0.62 1.16 0.98 Jaccard 0.70 0.35 0.37
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KaKs method: YN Pairs: 700
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Ka/Ks Quartiles Average P-value
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NA 16 Q1(Lower) 0.019 Ka 0.102 NA 48
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KaKs&lt;1 675 Q2(Median) 0.044 Ks 2.793 &lt;1E-100 419
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KaKs~1 0 Q3(Upper) 0.113 P-value 0.036 &lt;1E-10 85
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KaKs&gt;1 9 &lt;1.0 148
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KaKs~1 0 Q3(Upper) 0.113 P-value 0.036 &lt;1E-10 85
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KaKs&gt;1 9 &lt;1.0 148
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SEQUENCES: 707
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Average Lengths %GC CpG O/E
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5UTR CDS 3UTR 5UTR CDS 3UTR 5UTR CDS 3UTR
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bar 170.1 1612.4 230.2 39.0% 51.0% 38.5% 0.750 0.695 0.733
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bar 170.8 1612.4 229.6 39.1% 51.0% 38.4% 0.754 0.695 0.730
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fly 135.2 1520.2 314.4 36.8% 46.6% 35.5% 0.751 0.693 0.663
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foo 193.2 1539.8 336.8 40.5% 47.0% 36.7% 0.779 0.702 0.742
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Counts
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C1 C2 C3
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Cx Cy Cz
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bar 812,745 665,939 853,758
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fly 736,627 605,318 772,927
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foo 1,009,851 706,578 537,403
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Differential Expression (p-value &lt; 0.001)
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C1C2 C1C3 C2C3
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Differential Expression (p-value &lt; 0.001)
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CxCy CxCz CyCz
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bar 0 17 17
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fly 0 16 14
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foo 6 16 18
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----------------------------------------------------
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PROCESSING:
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AA: diamond --masking 0 --query-cover 25 --subject-cover 25
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AA: diamond --masking 0 --query-cover 25 --subject-cover 25
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NT: blastn -evalue 1e-05 -max_hsps 1 -max_target_seqs 25
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MSA: Score1=Sum-of-Pairs Score2=Wentropy

‎docs/ov/sDemo.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>sTCW_demoTra overview</title>
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<head><title>tra overview</title></head>
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<body>
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<center>
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<h2>Overview for sTCW_demoTra </h2>
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<table style="border: 1px solid black; border-spacing: 0px; border-collapse: collapse; width=700"><tr><td>
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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: 12,296 #GOs: 6,144 TPM Seq-DE GO-Enrich Pairs
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15-Mar-22 Build Database sequences loaded from external source
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15-Mar-22 Last Annotation with sTCW v4.0.0
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13-Jul-22 Build Database sequences loaded from external source
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13-Jul-22 Last Annotation with sTCW v4.0.3
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INPUT
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Counts:
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SEQID ID SIZE #REPS
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tra Stem 1,865,201 5
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tra Root 955,097 5
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tra Oleaf 474,551 5
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SEQID ID SIZE TITLE #REPS
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tra Stem 1,865,201 Tissue Stem 5
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tra Root 955,097 Tissue Root 5
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tra Oleaf 474,551 Tissue Old Leaf 5
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Sequences:
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SEQID SIZE TITLE AVG-len MED-len
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tra 211 Demo of assembled Illumina transcripts 1,079 861
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SEQID SIZE TITLE AVG-len MED-len
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tra 211 Demo of assembled Illumina reads 1,079 861
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ANNOTATION
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Hit statistics:
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ORF stats: Average length 862
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Has Hit 210 (99.5%) Both Ends 69 (32.7%) Multi-frame 6 (2.8%)
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Is Longest ORF 192 (91.0%) ORF&gt;=300 190 (90.0%) Stops in Hit 6 (2.8%)
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Markov Best Score 210 (99.5%) ORF=Hit 109 (51.7%) &gt;=9 Ns in ORF 1 (&lt;1%)
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Markov Best Score 210 (99.5%) ORF=Hit 103 (48.8%) &gt;=9 Ns in ORF 1 (&lt;1%)
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All of the above 191 (90.5%) with Ends 32 (15.2%)
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GC content: 48.65%
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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 15-Mar-22 diamond --masking 0
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sp invertebrates uniprot_sprot_invertebrates.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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sp fungi uniprot_sprot_fungi.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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sp bacteria uniprot_sprot_bacteria.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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sp full_BFIP uniprot_sprot_xBFxIxPxxx.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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tr plants uniprot_trembl_plants.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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tr invertebrates uniprot_trembl_invertebrates.fasta 27-Jan-21 15-Mar-22 diamond --masking 0
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sp plants uniprot_sprot_plants.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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sp invertebrates uniprot_sprot_invertebrates.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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sp fungi uniprot_sprot_fungi.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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sp bacteria uniprot_sprot_bacteria.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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sp full_BFIP uniprot_sprot_xBFxIxPxxx.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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tr plants uniprot_trembl_plants.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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tr invertebrates uniprot_trembl_invertebrates.fasta 21-Dec-21 13-Jul-22 diamond --masking 0
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Prune: none
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Gene ontology: go-basic.obo-Nov2021 GOdb: go_demo [GOs added with sTCW v4.0.0]
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Gene ontology: go-basic.obo-Nov2021 GOdb: go_demo [GOs added with sTCW v4.0.3]
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GO slim: goslim_plant
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ORF finder:

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