tamo2meme
Usage: tamo2meme [options] <matrix file>
Description:
Convert a TAMO file into a MEME version 4 formatted file suitable for use with MAST and other MEME Suite programs.
Input:
A TAMO file describes one or more motifs in terms of a Log-odds matrix and a set of sites that were used to make the motif. The script reads the sites and converts them into a position specific probability matrix.
A probability matrix and optionaly a log-odds matrix is output for each motif in the tamo file. 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 <TAMO ID>
- skip this ID (may be repeated)
- -numbers
- use numbers instead of strings as motif names
- -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 tamo ID is substituted for MOTIF_NAME; default: no url
Output:
Writes MEME format to standard output.
Sample Input:
Log-odds matrix for Motif 0 rGAA..TtctrGAA (0) # 0 1 2 3 4 5 6 7 8 9 10 11 12 13 #A 0.743 -1.052 1.647 1.443 -1.558 -0.374 -3.255 -5.001 -0.793 -2.480 1.175 -3.678 1.635 1.629 #C -1.105 -10.336 -8.324 -3.641 0.691 0.311 -1.463 -0.208 1.931 -1.053 -2.000 -10.641 -2.819 -4.350 #T -3.868 -3.114 -4.032 -2.297 0.288 -0.426 1.428 1.320 -2.576 1.393 -5.066 -3.566 -5.030 -3.764 #G 0.967 2.100 -4.305 -1.267 0.140 0.632 -1.563 -1.879 -2.088 -2.285 0.357 2.321 -8.368 -4.399 Sequence Logo # -------------- # -- 2.30 bits # G # G # GA GAA # GAA T C GAA # GAA TTCT GAA # AGAA TTCTAGAA # GGAA TTCTAGAA -- 0.29 bits # -------------- # rGAA..TtctrGAA Source: HSF1 Motif 0 rGAA..TtctrGAA (0) (Bits: 14.14 MAP: 0.00 D: 0.000 -1) E: 0.000 ch: 0.00 AAAAAACCAAAGAA 0 2.66564019036 AAAACACCACAGAA 0 6.34181478692 AGAACAGCCCAGAA 0 12.1162311612 AGAACCGCCGAGAA 0 11.5694520088 AGAACCTCCGAGAA 0 14.5611965064 AGAACCTGCTAGAA 0 16.5680637894 AGAACCTTCTAGAA 0 19.7669118865 AGAACCTTCTAGAA 0 19.7669118865 CGAACCTTCTAGAA 0 17.9190181888 CGAAGGTTCTAGAA 0 17.6896096981 GGAAGGTTCTAGAA 0 19.761489259 GGAAGGTTCTAGAA 0 19.761489259 GGAAGGTTCTCGAA 0 16.5861453685 GGAAGGTTCTGGAA 0 18.9435955025 GGAAGGTTCTGGAA 0 18.9435955025 GGAATGTTCTGGAA 0 19.0918355924 GGACTGTTCTGGAA 0 14.0084990288 GGAGTTTTCTGGAA 0 15.32449778 GGAGTTTTCTGGAA 0 15.32449778 GGATTTTTGTGGCC 0 -0.158188860768 ************** MAP Score: 0.000000