How to calculate identity percentage between proteins contained in a FASTA file?

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7 months ago

v.berriosfarias ▴ 140

Hello! I have a multiFASTA file that contains a set of aminoacidic sequences that I want to compare in terms of sequence identity, what tool do you recommend me for this? I want all vs all comparisons so I can build a heat map.

protein FASTA alignment • 484 views

ADD COMMENT • link updated 7 months ago by Ram 44k • written 7 months ago by v.berriosfarias ▴ 140

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clustal omega can calculate distance matrix between two proteins (makes sense if your proteins are of similar size). You could try that: https://static-bcrf.biochem.wisc.edu/tutorials/COVID19/spikealignment/book/distance-matrix.html

Also see --> percent identities for all by all protein alignment

ADD REPLY • link 7 months ago by GenoMax 147k

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This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for instance with BLAST)

ADD REPLY • link 7 months ago by b.contreras.moreira ▴ 310

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