ap_SequenceProfile

ap_SequenceProfile reads a Multiple Sequence Alignment (MSA) in ClustalO or FASTA format

and prints a sequence profile made from it. The program detects the format of ain input file by its extension: use either .fasta or .aln, for FASTA and ClustalO, respectively.

If the optional argument -w is used, sequences will be weighted before profile calculations. The profile probabilities will be therefore weighted counts rather than just raw observations.

USAGE: ./ap_SequenceProfile infile.aln [-w]

EXAMPLE: ./ap_SequenceProfile cyped.CYP109.aln ./ap_SequenceProfile cyped.CYP109.fasta -w

Keywords:

Categories:

  • core/data/sequence/SequenceProfile; core/protocols/SequenceWeightingProtocol
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