fasta-hamming-enrich [options] -w <word> -p <positives> -n <negatives>
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.
A word to determine enrichment.
Positive and negative sequences in FASTA format.
Writes a MEME motif file to standard output.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| Required | |||
| -w | word | The word to determine enrichment. | Required input. |
| -p | FASTA file | The positive sequences in FASTA format. | Required input. |
| -n | FASTA file | The negative sequences in FASTA format. | Required input. |
| General | |||
| -a | Alphabet 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). | ||
| -h | Print a help message and exit. | Runs as normal. | |