Question: How to get mouse multiple sequence alignments in fasta format
0
gravatar for Aimin Li
5.4 years ago by
Aimin Li30
Xi'an
Aimin Li30 wrote:

There are compressed multiple alignments of 59 assemblies to the mouse genome (mm10/GRCm38, Dec. 2011)
Readme and directory:
http://hgdownload-test.sdsc.edu/goldenPath/mm10/multiz60way/
MAF files:
http://hgdownload-test.sdsc.edu/goldenPath/mm10/multiz60way/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

mouse maf • 1.4k views
ADD COMMENTlink written 5.4 years ago by Aimin Li30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 969 users visited in the last hour