Hello Amit, It is true that sim4 only supports DNA, and not protein or translated data. PSL parsing is beyond the scope of this mailing list, however, you may find that the psl format itself is not very hard to parse. For more information on PSL format please see our PSL format FAQ:
http://genome.ucsc.edu/FAQ/FAQformat.html#format2 Note that the negative strand alignments are given in positive-strand coordinates for txStart and txEnd but the blockStarts are given in negative strand coords. This is done to make it easier to quickly look for overlapping alignments. But it often confuses users. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 7/3/12 3:16 AM, Mbandi S.K wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
