faffaf6750cf5492f3bd779a8e2d3fe4116e24d6 jnavarr5 Tue Jul 28 14:53:49 2026 -0700 Documenting the codonTable genomes.txt setting on the trackDb hub settings page and the track hub help page, with the changes page now linking to the new settings entry, refs #16550 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index cf700903439..39585a62e0f 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -7275,30 +7275,65 @@ <P><B>Example:</B></P> <pre> chromAuthority ucsc</pre> </DIV> <DIV class="chromSizes"><span class="types all"></span> <div class="format"><code>chromSizes <url/relativePath></code></div> <P>Defines a file to be used when displaying the sequences contained in an assembly. These are visible from the "View Sequences" link on the Gateway page, or with the "vs" keyboard shortcut when looking at the main Genome Browser image. </P> <P><B>Example:</B></P> <pre> chromSizes thisGenome.chromSizes.txt</pre> </DIV> +<DIV class="codonTable"><span class="types all"></span> +<div class="format"><code>codonTable default=<id> <sequenceName>=<id> ...</code></div> + <P>By default the Genome Browser translates codons to amino acids with the standard + genetic code, except for sequences named <code>chrM</code> or <code>chrMT</code>, which + use the vertebrate mitochondrial code. An assembly hub can assign a different + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi" target="_blank">NCBI + genetic code</a> to individual sequences with the <code>codonTable</code> setting in the + genome stanza.</p> + + <p>The value is a space-separated list of <code>sequenceName=id</code> pairs, where + <code>id</code> is an NCBI translation table number (for example 1 for the standard code, + 2 for vertebrate mitochondrial, 13 for ascidian mitochondrial). The special name + <code>default</code> sets the code used for any sequence not listed. Sequences with no + assignment keep the default behavior described above. This affects amino acid display in + the base position track's three-frame translation, in codon-colored annotation tracks such + as gene predictions, and on the details pages.</p> + + <p><B>Note</B>: <code>sequenceName</code> must be the sequence's own name as stored in the + assembly's <em>.2bit</em> file (the same name used in <code>chrom.sizes</code>), for + example a RefSeq or GenBank accession such as <code>NC_017929.1</code>. This is the + internal name even when a <code>chromAlias</code> and <code>chromAuthority</code> cause a + different name (such as <code>chrM</code>) to be displayed. Because the special + <code>chrM</code>/<code>chrMT</code> mitochondrial default only applies to sequences whose + own name is literally <code>chrM</code> or <code>chrMT</code>, an assembly whose + mitochondrial sequence has an accession name needs an explicit <code>codonTable</code> + entry to translate it with a mitochondrial code.</p> + + <p>See our assembly hub <a + href="/goldenPath/help/assemblyHubHelp.html#codonTable">codonTable</a> documentation for + more details.</p> + + <P><B>Example:</B></P> + <pre> codonTable default=1 NC_017929.1=13</pre> +</DIV> + <DIV class="defaultPos"><span class="types all"></span> <div class="format"><code>defaultPos <chr:start-end></code></div> <P>Defines the initial view in the Genome Browser, usually highlighting a popular gene or region of interest.</P> <P><B>Example:</B></P> <pre> defaultPos chr7:155799529-155812871</pre> </DIV> <DIV class="description"><span class="types all"></span> <div class="format"><code>description <str></code></div> <P>Description of the assembly version that is displayed on the Gateway page and title pages for this assembly. It also appears in the assembly pull-down menu.</P> <P><B>Example:</B></P> <pre> description July 2011 Castor bean</pre>