Apt way to perform multi pairwise alignments ?
2
0
Entering edit mode
8.3 years ago
deepue ▴ 160

I have 10 bacterial genomes and 78 virus genomes. I would like to identify if the virus is an insertion in one of the available bacterial genomes. To identify this, I am interested in calculating the similarity between all possible bacterial and virus genomes. What is the best possible way to do this, instead of looping over two sets of genomes ?

alignment genome • 1.6k views
ADD COMMENT
0
Entering edit mode
8.3 years ago
Benn 8.3k

I don't know if you want Needlemann-wunsch or smith-waterman, but take a look at the EMBOSS suite of tools for alignment

http://emboss.sourceforge.net/docs/

ADD COMMENT
0
Entering edit mode
8.3 years ago
abascalfederico ★ 1.2k

BLAST seems to be the best choice here. You can blast all your viral genomes agains all the bacterial genomes. Then you will need some rules to decide whether a similarity means a viral insertion (not necessarily)

ADD COMMENT

Login before adding your answer.

Traffic: 1321 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