.. _cli::p3-get-features-by-sequence:


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p3-get-features-by-sequence
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Find Protein Features Using Sequence Data
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.. code-block:: perl

     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 :ref:`cli-input-options`.

Additional command-line options are those given in :ref:`cli-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.