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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?