b86ab045ecfd00134c31978cb3196e7455e1c8c9 kuhn Tue Mar 29 12:31:55 2022 -0700 reworded slightly to clarify that it is not three variables PLUS the seq, the type and the db diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 36539d4..24c5a67 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -471,29 +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. -The URL requires 3 variables, the sequence to blat, the type of query and the database:</p> +The URL requires three variables: the sequence to blat, the type of query and the database, as follows</p> <pre> https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=[seq]&type=[type]&db=[database]&output=json</pre> <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> <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>