p3-sequence-profile

Profile Sequences by Letter Content

p3-sequence-profile.pl [options]

This script analyzes DNA or protein sequences in the key column of the incoming file and outputs the number of times each letter occurs. The output file will contain the letter in the first column and the count in the second, and will be sorted from most frequent to least. This can lead to very small output files.

Parameters

There are no positional parameters.

The standard input can be overridden using the options in Input Options.

Additional command-line options are those given in Column Options (to select the column containing the sequences) plus the following.

• fasta

Input file is a FASTA. In this case, the column specification will be ignored.

• count

The number of sequences will be output to STDERR.