Dear Galaxy, I was wondering whether I might be able to get the source of the online feature "Stitch MAF blocks", to use locally? Thanks you so much, in advance! Best regards, Stein Aerts VIB, Belgium Begin forwarded message: > *From: *Brooke Rhead <rhead(a)soe.ucsc.edu <mailto:rhead@soe.ucsc.edu>> > *Date: *Sat 31 Jan 2009 01:09:25 GMT+01:00 > *To: *Stein Aerts <stein.aerts(a)med.kuleuven.be > <mailto:stein.aerts@med.kuleuven.be>> > *Cc: *genome(a)soe.ucsc.edu <mailto:genome@soe.ucsc.edu> > *Subject: **Re: [Genome] Stitch MAF blocks given a set of genomic > intervals* > > Hello Stein, > > There is not a tool to do this in the Kent source tree. From one of > our developers: > > --- > We don't have good tools to do this, partially because the > transformation isn't necessarily possible (not all maf's can be > converted to a global alignment like FASTA is, and also maf blocks > don't necessarily contain all the sequence that are in the species). > > The user may grab the corresponding sequences using the maf, and run > their own global aligner (e.g. clustalw, MUSCLE). > --- > > You might be able to get Galaxy's source for this. If you haven't > already contacted them, their helpdesk address is > galaxy-user(a)bx.psu.edu <mailto:galaxy-user@bx.psu.edu>. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/30/09 03:25, Stein Aerts wrote: >> Hi, >> I am looking for a standalone solution to extract MAF blocks and >> then 'stitch' those together for each species into a fasta file, >> starting from a genomic interval of one species? Galaxy has this >> feature online so I was wondering whether there is a script or >> similar code in the Kent source (or a combination of scripts) to >> accomplish this locally in an efficient way? >> Many thanks in advance, >> Stein Aerts >> Belgium >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> _______________________________________________ >> Genome maillist - Genome(a)soe.ucsc.edu <mailto:Genome@soe.ucsc.edu> >> http://www.soe.ucsc.edu/mailman/listinfo/genome > Stein Aerts, PhD Laboratory of Neurogenetics VIB-KULeuven Belgium http://perswww.kuleuven.be/~u0038182/ <http://perswww.kuleuven.be/%7Eu0038182/> http://med.kuleuven.be/cme-mg/lng/ ------------------------------------------------------------------------ _______________________________________________ galaxy-user mailing list galaxy-user(a)bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user