Known motif finding given fasta sequences

usage: find_motif_seq.py [-h] [-j JID] -f FASTA [-m MOTIF_FILE]
                         [-p FIMO_CUTOFF]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        find_motif_seq_yli11_2020-09-27)
  -f FASTA, --fasta FASTA
                        input query fasta (default: None)
  -m MOTIF_FILE, --motif_file MOTIF_FILE
                        meme file (default:
                        /home/yli11/Data/Motif_database/Human/human.meme)
  -p FIMO_CUTOFF, --fimo_cutoff FIMO_CUTOFF

Summary

Identify known transcription factor binding sites on given sequences. Motif scanning is based on FIMO, default p-value is 1e-4.

Default known motifs are from Human. For mouse, use: /home/yli11/Data/Motif_database/Mouse/mouse_TF.meme

Input

Input fasta file.

>seq1
AAGTCGTA
>seq2
AAAAAAAAAAAAAAA

Usage

hpcf_interactive.sh
module load python/2.7.13
find_motif_seq.py -f input.fa

Output

Output is a tsv file. The first column is motif name, followed by sequence name. q-value column is empty. Last column is the matched sequence.

#pattern name   sequence name   start   stop    strand  score   p-value q-value matched sequence
motif1  seq1    12      26      -       15.9888 2.26e-06                GGAAGTCAGCCACCT
motif1  seq1    19      37      +       15.1667 3.2e-06         TGACTTCCCACTGTGTCCT

code @ github.