Hi Carsten,
I think our mafsInRegion utility might be what you're looking for. It
can be downloaded here: http://hgdownload.cse.ucsc.edu/admin/exe/
(choose your OS)
mafsInRegion - Extract MAFS in a genomic region
usage:
mafsInRegion regions.bed out.maf|outDir in.maf(s)
options:
-outDir - output separate files named by bed name field to outDir
-keepInitialGaps - keep alignment columns at the beginning and of a
block that are gapped in all species
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 10/31/11 5:38 AM, Carsten Raabe wrote:
> Dear all,
>
> I do face the following problem I would like to download certain regions
> (>>> RNA exons, detected by us)) of the human genome not only as simple
> fastA file containing the corresponding human genomic sequence (>>>
> which would know how to handle), but in addition I would like to extract
> these regions out of a whole genome alignment (mammal-wide) if possible.
> Furthermore I would like to sort the alignment out-put according my RNA
> exon orientation to perform phylogenetic analyses. I do have a custom
> made script for it however it works very slow which is mainly due to
> huge size of the alignment files.
>
> Sorry, I am afraid I might asked this one already however I failed to
> find an answer in the FAQ lists.
>
> Thanks a lot in advance and sorry for inconvenience I might have caused.
>
> Cheers,
>
> Carsten
>
>
> PS. I am afraid I might have asked this one already long time back,
> however I failed to find an answer in your FAQ lists or in my personal
> email.
>
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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