2ffb313fbbddc5b678beb8a92da4d513c178268d max Tue Apr 4 07:09:11 2023 -0700 got question from Jim R why long sequences do not work from IGV, so adding note to FAQ blat that HTTP POST is required for that, no redmine diff --git src/hg/htdocs/FAQ/FAQblat.html src/hg/htdocs/FAQ/FAQblat.html index 3e5a549..2c3eda2 100755 --- src/hg/htdocs/FAQ/FAQblat.html +++ src/hg/htdocs/FAQ/FAQblat.html @@ -475,25 +475,28 @@ <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 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> +If the sequence is longer than 8kbp, the request must be sent via HTTP POST. +</p> +<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=UUUCCCUUCCCCACUGUAGUGGGAGAGAAGGGAGUGGCCAUACCAUAUUUUUCUCGUGGGCCGUUGUAGUCAUAAGGCCUUCCUUUGCGGAAAAUUUUCAGGGUGGGAUA&type=translated%20RNA&db=hg38&output=json">https://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=UUUCCCUUCCCCACUGUAGUGGGAGAGAAGGGAGUGGCCAUACCAUAUUUUUCUCGUGGGCCGUUGUAGUCAUAAGGCCUUCCUUUGCGGAAAAUUUUCAGGGUGGGAUA&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>