25c2212f3f5f510ad207b568f8652b1732d0d816 lrnassar Mon Mar 28 15:03:20 2022 -0700 Clarifying that BLAT supports queries of 4 types, refs #27193 diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 875bbb5..36539d4 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -471,27 +471,29 @@ <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> +The URL requires 3 variables, the sequence to blat, the type of query and the database:</p> <pre> -https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=[seq]&type=DNA&db=[database]&output=json</pre> +https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=[seq]&type=[type]&db=[database]&output=json</pre> <p> -For example:</p> +Query types include DNA, protein, translated RNA and translated DNA:</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> +<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> +<a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNM&type=protein&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNM&type=protein&db=hg38&output=json</a> +<a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20RNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20RNA&db=hg38&output=json</a> +<a href="https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20DNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=TTTCCCTTCCCCACTGTAGTGGGAGAGAAGGGAGTGGCCATACCATATTTTTCTCGTGGGCCGTTGTAGTCATAAGGCCTTCCTTTGCGGAAAATTTTCAGGGTGGGATA&type=translated%20DNA&db=hg38&output=json</a> +</pre> <!--#include virtual="$ROOT/inc/gbPageEnd.html" --> </body>