In silico design and validation of a highly degenerate primer pair: a systematic approach

Journal, Genetic Engineering & Biotechnology
Prosper Obed ChukwuemekaOyeyemi Janet Oretade

Abstract

The techniques of amplifying genetic materials have enabled the extensive study of several biological activities outside the biological milieu of living systems. More recently, this approach has been extended to amplify population of genes, from evolutionarily related gene family for detection and evaluation of microbial consortial with several unique potentialities (e.g., enzymatic degradability). Conceivably, primer mixtures containing substitutions of different bases at specific sites (degenerate primers) have enabled the amplification of these genes in PCR reaction. However, the degenerate primer design problem (DPD) is a constraint to designing this kind of primer. To date, different algorithms now exist to solve various versions of DPD problem, many of which, only few addresses and satisfy the criteria to design primers that can extensively cover high through-put sequences while striking the balance between specificity and efficiency. The highly degenerate primer (HYDEN) design software program primarily addresses this variant of DPD problem termed "maximum coverage-degenerate primer design (MC-DPD)" and its heuristics have been substantiated for optimal efficiency from significant successes in PCR. In spite of the premiu...Continue Reading

References

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Aug 10, 2002·Bioinformatics·Chaim Linhart, Ron Shamir
Feb 28, 2004·Bioinformatics·Jain-Shing WuYow-Ling Shiue
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Jun 15, 2014·Applied and Environmental Microbiology·Luisa W HugerthAnders F Andersson

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Methods Mentioned

BETA
PCR

Software Mentioned

DPP
HYDENs
Geneious Prime
FAS
DegePrime
GeneFisher
hyden
Greene SCPrimer
DPD
FastPCR

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