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<p>The <spanclass="ttb">Include Row column</span> option is available because this column is alway present, but
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it may be desirable to exclude it in the output.
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<p>
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<spanclass="ttb">FASTA</span>: (Pairs Only) For each row, the two hit sequences from the <spanclass="ttx">Hstart</span> to <spanclass="ttx">Hend</span>
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are written to file. NOTE: this is a very slow function and takes minutes if many rows are selected.
<li>The report is on the genes in the query table; <i>hits without paired genes are ignored</i>.
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<p>
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<li>Unless the query is for <spanclass="ttb">Collinear</span>, <spanclass="ttb">Multi-hit</span> or <spanclass="ttb">Cluster genes</span>, a <spanclass="ttb">Gene</span>
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report will be produced.
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<li>This is most relevant when used with >2 species. <i><u>It has not been tested for >4 species.</u></i>
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<li><spanclass="ttb">Gene</span>, <spanclass="ttb">Collinear</span> and <spanclass="ttb">Multi-hit genes</span> produce a reference-based report whereas
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the <spanclass="ttb">Cluster genes</span> does not; however <spanclass="ttb">Cluster genes</span> shares most of the same options.
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<p><li>This is most relevant when used with >2 species. <i>It has not been tested for >4 species.</i>
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<p><li><spanclass="ttb">Gene</span>, <spanclass="ttb">Collinear</span> and <spanclass="ttb">Multi-hit genes</span>
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produce a <u>reference-based</u> report whereas the <spanclass="ttb">Cluster genes</span> does not;
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however <spanclass="ttb">Cluster genes</span> shares most of the same options.
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</ul>
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<aid="rint"></a>
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<h4>Reference-based interface</h4>
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<h4>Interface</h4>
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<p>The menu on the lower-right shows the options that will always exist.
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There may be additional options in between the middle lines,
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depending on the condition used to create the table, as discussed below.
Copy file name to clipboardExpand all lines: docs/Release.html
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@@ -54,6 +54,53 @@ <h3>Summary of recent major releases</h3>
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<tr><td><ahref="#v540">v5.4.0</a><td>(06-Apr-23)<td>Improved <spanclass="ttx">Cluster Hit</span> algorithm <spanclass="ttx">Algo1</span> for the detection of gene homology.
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</table>
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<aid="v586"></a>
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<h3>Release: v5.8.6 (15-July-2026)</h3>
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Changed to <spanclass="ttp">symap</span> and <spanclass="ttp">xToSymap</span> (including <spanclass="ttt">scripts/ConvertNCBI.java</span>
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and <spanclass="ttt">scripts/ConvertEns.java</span>).
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<p>
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<ul>
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<li><spanclass="ttp">xToSymap</span>:
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<ul>
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<li>Instead of using the first mRNA per gene, the following is done:
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<br>NCBI: use the longest mRNA.
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<br>Ensembl: use the mRNA with 'tag=Ensembl_canonical'; if none exist,
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use the longest mRNA.
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<li>The GFF output includes the CDS coordinates.
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<li><spanclass="ttl">All Seqs</span> option was added, which converts all sequences for SyMAP input.
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<br><spanclass="ttl">Include Protein-ID</span> option was removed.
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<li>Small things:
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<ul>
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<li>Instead of using the <spanclass="ttt">seqid</span> prefix 'Unk' for unknown sequences, the prefix 'Seq' is used.
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<li>NCBI: If a gff file has the scaffold NW_ prefix but the line contains 'chromosome',
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keep it a scaffold (it was tagging it a chromosome).
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<li>Ensembl: If a gene has no description, it will be given one of "uncharacterized protein".
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</ul>
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<li><spanclass="ttb">Summary</span>: Has various changes to improve the output.
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</ul>
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<p>
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<li><spanclass="ttp">Load Annotation</span>: If symap is started with the '-cds' flag, the CDS coordinates
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are loaded instead of the Exons. The only place this is obvious is on the
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<spanclass="ttp">Manager</span> and <spanclass="ttp">View</span>
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option for the species project; everywhere else will still say 'Exon'.
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<p>
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<li><spanclass="ttp">Queries</span>:
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<ul>
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<li>New options for <spanclass="ttx">Exact</span> and <spanclass="ttx">Start</span> for annotation.
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<li><spanclass="ttl">Export</span>: new option <spanclass="ttx">Unique splice genes</span>
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to export FASTA spliced genes, which also works for singles. If the annotation was loaded with
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<spanclass="ttp">symap</span> using the -cds flag,
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the output will be the spliced CDSs, else it will be the spliced exons.
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<li>Bug fix: (1) The <spanclass="ttl">Export</span> did not work for selected rows.
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(2) <spanclass="ttl">Show</span>
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crashed if using the <spanclass="ttl">Single</span> option.
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</ul>
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<p>
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<li><small>Developers: (1) ConvertNCBI and ConvertEnsembl were redesigned into classes. (2)
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Schema projects.types was changed from an enum to short string with types ncbi, ens, other.
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</small>
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</ul>
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<!-- ==================== -->
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<aid="v585"></a>
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<h3>Release: v5.8.5 (1-June-2026)</h3>
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More changes to the <spanclass="ttp">Linear</span> and <spanclass="ttp">Circle</span> control of displays.
Copy file name to clipboardExpand all lines: docs/SystemHelp.html
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<p><i>Make sure these two parameters are correct before running the alignment</i>: <spanclass="ttl">Minimum length</span>, <spanclass="ttl">Sequence files</span>.
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These are described in <ahref="#project">Load project</a>.
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<p>
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<p><spanclass="ttl">Sequence</span> and <spanclass="ttl">Anno</span> (annotation) <spanclass="ttl">files</span>:
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<br>If the files are put in the default locations, nothing needs to be entered for them.
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Default locations:
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</pre>
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See <ahref="./input/index.html" class="ext" target="_blank">input</a> for a description of the input files.
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</table>
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<p> <p>
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Note: as of v5.8.6, the <spanclass="ttp">xToSymap</span> conversion programs include CDS coordinates
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in the converted .gff files. If you start symap with the '-cds' option, the CDS coordinates will be loaded instead of
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the exons; the only evidence that they were used is on the project's <ahref="input/img/viewB.png">View</a> panel.
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