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I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command line actually) which has a similar output to the FASTA tool, i.e:

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For my use case, the 'Source' column is not super relevant, so it does not matter if it's not included in the output. What's most important is the DB:ID and the match statistics.

Have you used anything similar? Do you have any suggestions regarding such a tool? Thanks in advance!

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  • $\begingroup$ Hmmm ... two suggestions, you can do both via Python, Blast or a tree matrix. Its an interesting question but difficult to know what you're looking for $\endgroup$
    – M__ ♦
    Commented Feb 18, 2022 at 21:13
  • $\begingroup$ Will you be comparing specific, known sequences, or is part of the question finding similar sequences to your query in a large database of non-related sequences? Basicaly, do you want a sequence aligner (mafft, t_coffee, clustal etc) or tools like the various flavors of blast (psi-blast, p-blast)? Or are you looking for proteins with shared domains which means tools like HMMER or psi-blast again? Pretty much everything in bioinformatics can be done from the command line, so you need to explain exactly what question you're trying to answer for us to suggest the better options. $\endgroup$
    – terdon ♦
    Commented Feb 20, 2022 at 12:28

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Apparently there is a REST API for FASTA. Looks like there are few dependencies but other than that should be straightforward to use.

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