Fwd: [Genome] Stitch MAF blocks given a set of genomic intervals
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@soe.ucsc.edu> Date: Sat 31 Jan 2009 01:09:25 GMT+01:00 To: Stein Aerts <stein.aerts@med.kuleuven.be> Cc: 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@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@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://med.kuleuven.be/cme-mg/lng/
Hello Stein, All of the Galaxy source code is freely available for download - instructions are at http://g2.trac.bx.psu.edu/wiki/HowToInstall. All of the Galaxy tools that are included in the distribution can be executed from the command line. The "Stitch MAF blocks" tool is available in the distribution at ~/tools/maf/interval_maf_to_merged_fasta.py. Greg Von Kuster Galaxy Development Team Stein Aerts wrote:
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@soe.ucsc.edu <mailto:rhead@soe.ucsc.edu>> *Date: *Sat 31 Jan 2009 01:09:25 GMT+01:00 *To: *Stein Aerts <stein.aerts@med.kuleuven.be <mailto:stein.aerts@med.kuleuven.be>> *Cc: *genome@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@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@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/
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