All of the Galaxy source code is freely available for download -
instructions are at
. 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:
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!
Begin forwarded message:
> *From: *Brooke Rhead <rhead(a)soe.ucsc.edu <mailto:email@example.com>>
> *Date: *Sat 31 Jan 2009 01:09:25 GMT+01:00
> *To: *Stein Aerts <stein.aerts(a)med.kuleuven.be
> *Cc: *genome(a)soe.ucsc.edu <mailto:firstname.lastname@example.org>
> *Subject: **Re: [Genome] Stitch MAF blocks given a set of genomic
> 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:email@example.com>.
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> On 01/30/09 03:25, Stein Aerts wrote:
>> 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
>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>> Genome maillist - Genome(a)soe.ucsc.edu <mailto:Genome@soe.ucsc.edu>
Stein Aerts, PhD
Laboratory of Neurogenetics
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