Hello, What you are seeing is the expected display.
If there is no splicing, then it does not have a "direction" even though it will have a strand, those are the arrows in the sequence block in the display. The strand is the strand being viewed. BLAT doesn't know if the sequence is a 5' or 3' read with respect to the transcript/gene. So, it will compliment if necessary. As you noticed, the compliment and strand information is included in the regular text BLAT output/display. Hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Janet Young" <[email protected]> wrote: > From: "Janet Young" <[email protected]> > To: [email protected] > Sent: Monday, August 31, 2009 7:21:57 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] BLAT browser strand display for intronless query seqs > > Hi, > > I'm not sure if I have a suggestion to add a feature to the browser, > > or if I'm asking about a feature that already exists but I can't find > > it. > > I have a bunch of sequences I'm BLATting, some of which match the > forward strand and some match reverse (with respect to the assembly) . > > None have introns or any other interruption to the match. I can see > > the strand on the BLAT summary page but not when I go to the browser - > > it'd be really useful to show it there too. If there's an intron or > > other interruption to the match I can see strand displayed by arrows > > in the intron, but without for perfect matches I don't see the strand > > displayed. > > The example below will help show what I mean when BLATted to the mouse > > assembly (any version) - they're from opposite strands, but you can't > > see that when you go to the browser display. > > thanks for any suggestions, > > Janet Young > > ------------------------------------------------------------------- > > Dr. Janet Young (Trask lab) > > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., C3-168, > P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 > email: jayoung ...at... fhcrc.org > > http://www.fhcrc.org/labs/trask/ > > ------------------------------------------------------------------- > > > >test1 > AAGGTTTTTAGTTCTGTCTACAATCACAGGTACCTTTTTTCATACAGGTTGTGGTCTTAGAATGTACTTGGC > > AGAAGTTGGAGCTGCCTTACAAGGCCATTTCAAGATCCATGGTGAATTTTACCTGTAAGAGAAGAAAAATATTCTCATGGCTTTATACTGAAGAATGTACATGTGGACTAATGATCCTACGACAGGCATAAAAGAAATGCCTGGTGCAGAATAAGAGAGCAGACAATGATAATTATATATACAACAATATATTACCTCATATGCTCTGAAGCCTCTTATTTTTTAAATACTTGTAGAAATGATGAAGCCTACATCAAACCCTTAAGACAGTGAGAGGAAGACAGAGTATTTGGGTGAATTGAGTCAAATATTTAATGCACTTATCTTATTGCATGCAATACAATGTGGATGCTTAGGTGCCTCAGAAAGTCTTCCTATGGTGTTATATTGAGGTGTAGGAAGGTAGAGGCTCAAGATACCTAAAAAAGAGTATATCTTATGCACATAATTTTAGCATCATTTTAATGTTTCTTTAGAAAAATGAACAATAGTTTGAAGTAATATTTTCATTATTTACTATTTTATCTTTGATTTTGAACATGGTTTTTCAATTTGATTTAAAATTAGATTGGAAAGTCCTCTTACATCAACCATACTAGCTATCATCAATTAACAAAATAAGTTATTTTTGGATGTCCTATATTCTTCTGGAAAACCAAAACCATATCACTGGCTTTCAGTAAACAATGAAGAATTCCAAAGTACACCATAGCTTGTAGATGCTCCTTAGGGAGGGTCAGCCAGGCCTTAATGAGTAACTTTGTTCCAGTTATTATTTCTGCATAAAAAAAGCCAAAGAACCTGTCTCTCAAAGGGGCAGGCAGCAATAGCCCCAAGGGTTTGTTATGCTTACCCAGAGCCCCTTTCTCTCTCTTTATGCTCAAAGATATTGACCTTCATTCCTGCTGCATGTGCATCTTTGGCAGAG > >test2 > TCTGCCAAAGATGCACATGCAGCAGGAATGAAGGTCAATATCTTTGAGCATAAAGAGAGAGAAAGGGGCTCT > > GGGTAAGCATAACAAACCCTTGGGGCTATTGCTGCCTGCCCCTTTGAGAGACAGGTTCTTTGGCTTTTTTTATGCAGAAATAATAACTGGAACAAAGTTACTCATTAAGGCCTGGCTGACCCTCCCTAAGGAGCATCTACAAGCTATGGTGTACTTTGGAATTCTTCATTGTTTACTGAAAGCCAGTGATATGGTTTTGGTTTTCCAGAAGAATATAGGACATCCAAAAATAACTTATTTTGTTAATTGATGATAGCTAGTATGGTTGATGTAAGAGGACTTTCCAATCTAATTTTAAATCAAATTGAAAAACCATGTTCAAAATCAAAGATAAAATAGTAAATAATGAAAATATTACTTCAAACTATTGTTCATTTTTCTAAAGAAACATTAAAATGATGCTAAAATTATGTGCATAAGATATACTCTTTTTTAGGTATCTTGAGCCTCTACCTTCCTACACCTCAATATAACACCATAGGAAGACTTTCTGAGGCACCTAAGCATCCACATTGTATTGCATGCAATAAGATAAGTGCATTAAATATTTGACTCAATTCACCCAAATACTCTGTCTTCCTCTCACTGTCTTAAGGGTTTGATGTAGGCTTCATCATTTCTACAAGTATTTAAAAAATAAGAGGCTTCAGAGCATATGAGGTAATATATTGTTGTATATATAATTATCATTGTCTGCTCTCTTATTCTGCACCAGGCATTTCTTTTATGCCTGTCGTAGGATCATTAGTCCACATGTACATTCTTCAGTATAAAGCCATGAGAATATTTTTCTTCTCTTACAGGTAAAATTCACCATGGATCTTGAAATGGCCTTGTAAGGCAGCTCCAACTTCTGCCAAGTACATTCTAAGACCACAACCTGTATGAAAAAAGGTACCTGTGATTGTAGACAGAACTAAAAACCTTA > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
