Motif-Mark

Given a a list of gene sequences and motifs, this program will produce an image to visualize the locations of each motif across the gene sequences.

Input

1. FASTA file with gene sequences
   • Maximum of 10 sequences (≤1000 bases each)
   • Exons should be indicated by uppercase letters and introns by lowercase letters
2. Text file with a list of motifs to search
   • One motif per line
   • Maximum of 5 motifs (≤10 bases each)

Argparse options:

-f, --fasta: required arg, file path to FASTA file
-m, --motifs: required arg, file path to motif text file

How to format input files:

FASTA:

>INSR chr19:7150261-7150808 ctctgtcctcaaaggcgttggttttgtttccacagAAAAACCTCTTCAGGCACTGGTGCCGAGGACCCTAGgtatgactcacctgtgcgacccctgg
>MBNL chr3:152446461-152447003 atgttaatgcgcttgaaccccactggcccattgccatcatgtgctcgctgcctgctaattaagACTCAGTCGGCTGTCAAATCACTGAAGCGACCCCTCGAGGCAACCTTTGACCTGgtactatgacctttcaccttttagcttggcatgtagctttattgtagatacaagttttttttt

Motifs:

ygcy
GCAUG
catag
YYYYYYYYYY

Example of how to run the program:

python motif-mark-oop.py -f Figure_1.dnas -m Fig_1_motifs.txt 

Output

The program will output a single image (.png) containing each of the inputted sequences with motifs, introns, and exons to scale depending on their lengths. An example of the output can be seen below where exons are indicated by the black boxes and introns are indicated by the grey line.