Automated Design and Scoring of Degenerate Primers From Multiple Taxon-Specific Primers Den Ivanov BIO 131, Spring 2017
The Problem Given a list of taxon-specific primers, how can I create an algorithm that can create one set of degenerate primers that represent that whole list?
How did I try to solve it?
Where’d I get my data?
High Level Steps • Inputs: threshold value, primers, scoring matrix • Split text document (each primer on a line) into a list of strings • Create count matrix of # of each nucleotide at each position • Use math.isclose to determine if any nucleotides are within a given threshold • Calculate degenerate primer based on this • Score using modified partial hamming algorithm (based off of scoring matrix)
Scoring Matrix
Results!
Questions?
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