Apt way to perform multi pairwise alignments ?

Question

[deepue]

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 ?

Answer 1

[Benn]

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/

Answer 2

[abascalfederico]

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)