172860595b76a888af59d255a98233983f2b14e1 lrnassar Thu Mar 24 14:23:57 2022 -0700 Adding entry about JSON url format for blat, refs #27193 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index adf6c3e..875bbb5 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -15,30 +15,31 @@ <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> +<li><a href="#blat14">Querying BLAT programmatically using URLs</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 @@ -466,17 +467,31 @@ 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 website</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> +<a name="blat14"></a> +<h2>Querying BLAT programmatically using URLs</h2> +<p> +For programmatic access, BLAT supports URL queries which are returned as psl format in a JSON structure. +This is only available for DNA queries. The URL requires 2 variables, the sequence to blat and +the database:</p> +<pre> +https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=[seq]&type=DNA&db=[database]&output=json</pre> +<p> +For example:</p> +<pre> +<a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=GACCTCGGCGTGGCCTAGCG&type=DNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=GACCTCGGCGTGGCCTAGCG&type=DNA&db=hg38&output=json</a></pre> +</p> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> </body>