Name: DiNAMO
Owner: Bonsai team
Description: Discriminative DNA IUPAC motif discovery tool
Created: 2017-04-19 13:07:29.0
Updated: 2017-06-27 11:22:57.0
Pushed: 2017-11-21 14:54:15.0
Size: 3073
Language: C++
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences. It has two modes: scanning mode (default), where all windows are parsed, or fixed-position mode (see optional parameter -p ), where only motifs occurring at a specific position in the sequences are taken into account.
DiNAMO can be used in a variety of applications, such as ChIP-seq peak analysis for transcription factor binding sites identification, or finding motifs that induce systematic sequencing errors.
Boost library (if not in the standard includes, please use -I /path/to/boost in the Makefile)
make
The executable file is located in the bin/ directory
DiNAMO takes as input two fasta files, which contain respectively the positive dataset (signal.fa) and the negative dataset (control.fa). You should specify also the motif length '-l'. Optionally, you can provide a maximum number of degenerate letters '-d'. The output file contains the over-represented motifs found in the positive dataset compared to the negative dataset, in the MEME format (see http://meme-suite.org/doc/meme-format.html).
dinamo -pf signal.fa -nf control.fa -l 6
maximum number i of degenerate letters
-d <i>
Only process motifs at a offset i (0..N) related to the end of each sequence
-p <i>
output file
-o <file>
change Fisher's exact test p-value threshold f (default: 0.05)
-t <f>
do not display logs
--no-log