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Get specific sequences from a multi-FASTA file.

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A command-line utility to manipulate biological sequences from a multi-FASTA file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only.

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  • collect only some sequences out of a large multi-FASTA file
  • get sequence number N only, regardless of ID
  • complement mode: return all sequences that are NOT in the list of IDs
  • "matching" mode: choose which part (between | characters) of the ID should match
  • sequence names provided one per line in a text file (first word in line used, or whatever is given to the -k option)
  • the > symbol is ignored if it is present in the beginning of IDs in the list (useful if using FASTA identifiers)
  • if only one sequence is needed, its ID can be given directly to the -l option (no need of a file)
  • add a suffix to IDs before searching (useful when IDs come from proteins that have _1 in the ID, but genes do not)
  • compressed sequence database files (-s) are supported
  • quite mode, output only important warnings and errors


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