motif-mark

Motif Mark assignment for BI625

motif-mark-oop.py is a Python script which uses object-oriented code to produce a visualization of nucleotide motifs on gene sequences.

Run Requirements

The script must be run in a conda environment with pycairo installed.

Input Requirements

• -f: A FASTA file containing gene sequences
  • Up to 10 gene sequences
  • Each sequence up to 1000 nucleotides in length
  • Exons denoted as CAPITAL nucleotides, otherwise lowercase nucleotides
• -m: A text file containing motif sequences
  • Up to 5 motifs
  • One motif sequence per line
  • Motifs should use IUPAC nucleotide notation

Output

• The script will output a png figure displaying genes, exons, and motifs to scale.
  • Genes are represented by a black line in the final image.
  • Exons are represented by a semitransparent gray rectangle at the corresponding position on the gene line.
  • Motifs are indicated by colored semitransparent markings along the black gene line.

Considerations

• The script will identify motifs with degenerate nucleotides that are coded according to IUPAC notation.
• The script will identify overlapping motifs; the overlap will be visible with semitransparent colors on the final figure.