fasta-hamming-enrich

Usage:

fasta-hamming-enrich [options] -w <word> -p <positives> -n <negatives>

Description

Compute the Hamming distance from <word> to each FASTA sequence in the positive and negative files. Apply Fisher's Exact test to each distance. <word> may contain ambiguous characters.

Input

A word to determine enrichment.

Positive and negative sequences in FASTA format.

Output

Writes a MEME motif file to standard output.

Options

Option Parameter Description Default Behavior
Required
-wword The word to determine enrichment. Required input.
-pFASTA file The positive sequences in FASTA format. Required input.
-nFASTA file The negative sequences in FASTA format. Required input.
General
-aAlphabet file Specify the alphabet definition. Sequences will be verified to be in the given alphabet. The standard DNA alphabet is assumed.
-r  Refine the consensus by using a branching search (distance 1 steps; beam size = 1).