rna2meme

Usage: rna2meme [options] <FASTA file>

Description:

Convert an RNA sequence to its binding motif in MEME format.

Input:

FASTA file containing short RNA sequences.

Options:

-start <offset>

starting offset in rna sequence (inclusive); use negative numbers to count from end; default: 1

-end <offset>

ending offset in rna sequence (inclusive); use negative numbers to count from end; default: -1

-match <count>

count to assign to a match (complement); default: 1

-wobble <count>

count to assign to a U for a G, or a G for a U; default: 0.1

-miss <count>

count to assign to a non-match non-wobble; default: 0.01

-bg <background file>

file with background frequencies of letters; default: uniform background

-pseudo <total pseudocounts>

add <total pseudocounts> times letter; background to each frequency; default: 0

-logodds

output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only

-url <website>

website for the motif; The FASTA ID is substituted for MOTIF_NAME; default: no url

Output:

Writes MEME format to standard output.