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

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

Apr 04, 2024 103 likes •204 views

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

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Automated Design and Scoring

  • f Degenerate Primers From

Multiple Taxon-Specific Primers

Den Ivanov BIO 131, Spring 2017

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The Problem

Given a list of taxon-specific primers, how can I create an algorithm that can create one set

  • f degenerate primers that represent that

whole list?


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How did I try to solve it?

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Where’d I get my data?

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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)

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Scoring Matrix

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Results!

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Questions?