rna2meme

Usage:

rna2meme [options] <sequence file>

Description

Convert each RNA sequence in the input to a DNA motif in MEME motif format.

Input

<sequence file>

The name of 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 Behavior
General Options
-rna  Output RNA motifs instead of DNA motifs. Output DNA motifs.
-seed_startoffset The starting offset of the seed in the (micro-)RNA sequence. If this value is 0, the entire sequence is treated as the seed (see -other_count below). 0: the entire RNA sequence is treated as the seed.
-seed_endoffset The ending offset of the seed in the (micro-)RNA sequence. This option is ignored if -seed_start is 0. 0
-startoffset The starting offset in the RNA sequence (inclusive). Use negative numbers to count from the end. Do not use this option in conjunction with -seed_start. No starting offset is used.
-endoffset The ending offset in RNA sequence (inclusive). Use negative numbers to count from end. Do not use this option in conjunction with -seed_start. 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.
-other_countcount Extra count to add to match, wobble and misses in the non-seed regions. Setting this to a large value reduces the effect of poor matching in the non-seed regions; setting this to zero causes seed and non-seed regions to be weighted equally. 0.5