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Apt way to perform multi pairwise alignments ?

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
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updated by abascalfederico abascalfederico • written by deepue deepue

2 answers

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/

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updated by Ram Ram • written by Benn Benn

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)

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updated by Ram Ram • written by abascalfederico abascalfederico

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