Apt way to perform multi pairwise alignments ?
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8.8 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 • 1.7k views
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8.8 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/

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8.8 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)

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