rna2meme

Usage:

rna2meme [options] <sequence file>

Description

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

Input

Sequence File

A file containing short FASTA formatted RNA sequences. If the file name is '-' then the file is read from standard input.

Output

Options

Option Parameter Description Default Behaviour
General Options
-startoffset The starting offset in the RNA sequence (inclusive). Use negative numbers to count from the end. No starting offset is used.
-endoffset The ending offset in RNA sequence (inclusive). Use negative numbers to count from end. No ending offset is used.
-matchcount The count to assign to a match (complement). A count of 1 is used.
-wobblecount The count to assign to a U for a G, or a G for a U. A count of 0.1 is used.
-misscount The count to assign to a non-match non-wobble. A count of 0.01 is used.