Priority List of Topics

perl scripts for genome analysis

PWM Scan - a perl script that scans a genome or long DNA sequence for motifs that fit into a specific position weight matrix's parameters. Includes a quicker scan and a longer scan that uses every possible window.

Blast Parse - python script that will parse local blast results. Input should be the tab delimiter format as follows: QueryName Subject QueryEnd QueryStart SubjectEnd. Output can sort by any one of these elements. The default setting is to sort by Subject (in our case contigs or scaffolds). Note: to run, edit input file name to match your input file. Then type "python /pathto/blastparse.py" from terminal