p3-get-features-by-sequence

Find Protein Features Using Sequence Data

p3-get-features-by-sequence.pl [options]

This script takes as input a file containing DNA or protein sequences and finds features with those identical sequences. For a DNA sequence, it is somewhat limited in that it will only find features in organisms with a genetic code of 4 or 11.

The program processes one sequence at a time, so has poor performance for a large input file.

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 specify the input column containing the sequence) plus the following options.

• dna

The input contains DNA sequences. This is the default.

• protein

The input contains protein sequences. This is mutually exclusive with DNA.

• fasta

The input file is a FASTA. In this case the output file will be tab-delimited with the columns being (1) the sequence ID, (2) the sequence comment, and (3) the found feature ID.