How to calculate identity percentage between proteins contained in a FASTA file?
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.
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v.berriosfarias •
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clustal omegacan 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.htmlAlso see --> percent identities for all by all protein alignment
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)