Automated Design and Scoring of Degenerate Primers From Multiple - PowerPoint PPT Presentation

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?