How to get multiple alignments from different species using lastz?
0
0
Entering edit mode
7.8 years ago
Cacau ▴ 520

For example, I want to perform multiple genome alignment for cat, dog and cow using lastz. How should I specify the argument to run alignment for all of them?

Or should I run pairwise lastz and then combine the results? If so, how should I do?

alignment • 2.4k views
ADD COMMENT
0
Entering edit mode

Lastz is a pair-wise aligner.

Have you looked at the pre-computed alignments from UCSC (scroll down the page and find multiple-alignments) or Ensembl (these are pairwise alignments with synteny analysis for some) for vertebrate genomes?

ADD REPLY
1
Entering edit mode

Pre-computed alignments are not available for domestic water buffalo (Bubalus bubalis) in UCSC or ensemble. I want to create a maf file for buffalo with human, cow and dog. Is there any tutorial links on how to perform multiple alignment on genomes? What may be memory requirement to do the same?

ADD REPLY
0
Entering edit mode

Do you find any solution or option to do the same?

ADD REPLY

Login before adding your answer.

Traffic: 2426 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