How to get mouse multiple sequence alignments in fasta format
0
0
Entering edit mode
11.2 years ago
Aimin Li ▴ 30

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

maf mouse • 2.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 1755 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6