e674e530d83be9a0408a4e35c8940547c0b07a8b gperez2 Fri Mar 5 10:12:57 2021 -0800 Adding documentation for Protein-translated BLAT having different results, refs #26658 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index f45f743..c90268b 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -14,30 +14,31 @@ <li><a href="#blat1b">BLAT cannot find a sequence at all or not all expected matches</a></li> <li><a href="#blat1c">BLAT or In-Silico PCR finds multiple matches such as chr_alt or chr_fix even though only one is expected</a></li> <li><a href="#blat2">BLAT use restrictions</a></li> <li><a href="#blat3">Downloading BLAT source and documentation</a></li> <li><a href="#blat5">Replicating web-based BLAT parameters in command-line version</a></li> <li><a href="#blat6">Using the <em>-ooc</em> flag</a></li> <li><a href="#blat4">Replicating web-based BLAT percent identity and score calculations</a></li> <li><a href="#blat7">Replicating web-based BLAT "I'm feeling lucky" search results</a></li> <li><a href="#blat8">Using BLAT for short sequences with maximum sensitivity</a></li> <li><a href="#blat9">BLAT ALL genomes</a></li> <li><a href="#blat10">BLAT ALL genomes: No matches found</a></li> <li><a href="#blat11">Approximating web-based BLAT results using gfServer/gfClient</a></li> <li><a href="#blat12">Standalone or gfServer/gfClient result start positions off by one</a></li> +<li><a href="#blat13">Protein-translated BLAT having different results</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a></p> <a name="blat1"></a> <h2>BLAT vs. BLAST</h2> <h6>What are the differences between BLAT and BLAST?</h6> <p> BLAT is an alignment tool like BLAST, but it is structured differently. On DNA, BLAT works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. By default, the index consists of all non-overlapping 11-mers except for those heavily involved in repeats, and it uses less than a gigabyte of RAM. This smaller size means that BLAT is far more easily @@ -445,17 +446,30 @@ <a name="blat12"></a> <h2>Standalone or gfServer/gfClient result start positions off by one</h2> <h6>My standalone Blat results or gfServer/gfClient Blat results have a start position that is one less that what I see on web Blat results</h6> <p> This is due to how we store internal coordinates in the Genome Browser. The default Blat <strong>Output type</strong> of <strong>hyperlink</strong> shows results in our internal coordinate data structure. These internal coordinates have a zero-based start and a one-based end. See the following <a target="_blank" href="/FAQ/FAQtracks#tracks1" >FAQ entry</a> for more information.</p> <p> If the <strong>Output type</strong> is changed to <strong>psl</strong> on web Blat, the same zero-based half open coordinate results will be seen as the standalone Blat and gfServer/gfClient procedures.</p> +<a name="blat13"></a> +<h2>Protein-translated BLAT having different results</h2> +<p> +Protein-translated BLAT (protein or translated RNA queries) uses the standard vertebrate +genetic code. It will be slightly less sensitive on mitochondria and species using other +genetic codes. More information on standard genetic codes can be found on the +<a target="_blank" +href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes"> +NCBI The Genetic Codes page</a>. Additional details on mitochondria codon tables can be found on +the <a target="_blank" +href="https://www.wikiwand.com/en/DNA_and_RNA_codon_tables">Wikiwand website</a>. +</p> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> </body>