Dear ALL, I noticed that BLAT-six-frames does not support the sim4 format. I have been parsing the sim4 format and have to deal now with psl unfortunately. Has anyone on this list written a parser for BLAT-six-frame ? I would appreciate any help (in perl if possible) from which I can expand further.
I would also like to know what genetic code in being used for conceptual translation. Does anyone know where I can find pslCoverage, pslFilter, pslCDnaFilter, pslMrnaCover and pslHitPercent? I checked the achieve and noticed a mail sent by Jennifer (Wed May 12 10:55:49 PDT 2010) which says pslCoverage is fairly old and is not recommended for use anymore. I am comparing two transcriptomes ( say two sets of ESTs) to evaluate the linearity between them. I am using blat in two modes: -q=dna -t=dna && -q=rna & -t=prot . In these instances, the idea is to compare two sets of strings. Is there anything wrong in these modes regarding what I wish to achieve? Any suggestion thereof will be highly appreciated. Many thanks Mbandi S.K -------------------------------------------- Universiteit van Wes-Kaapland Suid-Afrika > Since that combination is not supported by BLAT, > swap the target database and query: > blat -t=dnax dna_query.fa -q=prot proteome.fa output.psl > -Galt > On Wed, Jun 27, 2012 at 12:31 PM, Steve Heitner <[email protected]> wrote: >> Hello, Amit. >> Since that combination is not supported by BLAT, go ahead and swap the target database and query as in your original email. >> Please contact us again at [email protected] if you have any further questions. >> --- >> Steve Heitner >> UCSC Genome Bioinformatics Group >> From: Amit Pande [mailto:[email protected]] >> Sent: Wednesday, June 27, 2012 2:05 AM >> To: [email protected] >> Subject: Re: [Genome] BLAT - six frames >> Hello Steve, >> I already tried what you wrote to me but it gives me the following error: >> Loaded 22243362 letters in 51824 sequences >> Unrecognized combination of target and query types >> It works if I switch -q with -t, but it wouldn't be correct this way....would it ? >> warm regards, >> Amit. >> On Tue, Jun 26, 2012 at 10:29 PM, Steve Heitner <[email protected]> wrote: >> Hello, Amit. >> You were very close. You just need to reverse your database and query options. The correct command should be: >> blat -t=prot proteome.fa -q=dnax dna_query.fa output.psl >> Please contact us again at [email protected] if you have any further questions. >> --- >> Steve Heitner >> UCSC Genome Bioinformatics Group >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On >> Behalf Of Amit Pande >> Sent: Tuesday, June 26, 2012 2:23 AM >> To: [email protected] >> Subject: [Genome] BLAT - six frames >> Dear Curators, >> I am trying to run BLAT locally on the command line. I have a query file >> which consists of DNA and a database file which has proteome. >> I am using dnax option because I want the query to be translated in 6 frames >> to protein and then align it to the database. >> The command I am typing is: >> blat proteome.fa dna_query.fa -t=dnax -q=prot output.psl >> I am not sure about the results, kindly tell me whether this is the right >> way to execute the program . >> Thank you in advance, >> warm regards, >> Amit. >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
