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-   -   How to get mouse multiple sequence alignments in fasta format (http://seqanswers.com/forums/showthread.php?t=43610)

emanlee 05-26-2014 05:44 AM

How to get mouse multiple sequence alignments in fasta format
 
There are compressed multiple alignments of 59 assemblies to the mouse genome (mm10/GRCm38, Dec. 2011)
Readme and directory:
http://hgdownload-test.sdsc.edu/gold...0/multiz60way/
MAF files:
http://hgdownload-test.sdsc.edu/gold...ltiz60way/maf/

We have thousands of mouse transcripts in bed format (file name: mouse.bed).
How can we get the alignments in FASTA format for all the mouse transcripts as follows
(we only need the specified five species, not all the 60 species):

>mm10|chr6(+):2345-7890
ATCGAAAATTGCCCAAA...
>oryCun2
AT-GAAAAT-GCCCAAA...
>speTri2
--CGAAAATTGCCCAAA...
>hg19
ATCGAAAATTGC-----...
>otoGar3
ATCGAAA----CCCAAA...


Thanks a lot, in advance.

Aimin Li


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