Hello Stein,
There is not a tool to do this in the Kent source tree. From one of our developers:
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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).
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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.
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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
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