chen2meme

Usage: chen2meme [options]

Description:

Read a CHEN matrix file and convert to MEME format. You may concatenate files for more than one motif.

Input:

Reads standard input.

Concatenated CHEN files describe one or more motifs. Each motif has a header line and a position-weight matrix.

A probability matrix and optionally a log-odds matrix are output for each motif. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.

Options:

-skip <ID>

skip this ID (may be repeated)

-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

print log-odds matrix, too; default: print frequency matrix only

-url <website>

website for the motif; The motif name is substituted for MOTIF_NAME;

-h

print usage message

Output:

Writes MEME format to standard output.

Sample Input:

>NANOG
2       64      4       10
1       66      1       12
52      1       0       27
0       0       0       80
0       0       0       80
0       5       74      1
3       1       1       75
3       49      14      14
57      9       0       14
1       0       3       76
1       3       46      30
4       48      12      16
30      16      3       31
31      12      19      18
41      12      12      15
16      20      12      32
>OCT4
11      216     13      99
168     10      1       160
1       6       2       330
12      0       8       319
21      92      213     13
98      5       5       231
68      93      37      141
326     0       4       9
0       0       0       339
0       0       319     20
4       289     19      27
288     1       1       49
212     25      73      29
294     8       23      14
55      28      54      202