PriFi -- using a multiple alignment of related sequences to find primers for amplification of homologs

What you can do:
Design PCR primers based on multiple sequence alignment of homologous DNA sequences.
Highlights:
  • This program designs pairs of primers useful for PCR amplification of genomic DNA in species where prior sequence information is not available.
  • The program works with an alignment of DNA sequences from phylogenetically related species and outputs a list of possibly degenerate primer pairs fulfilling a number of criteria, such that the primers have a maximal probability of amplifying orthologous sequences in other phylogenetically related species.
  • Operating on a genome-wide scale, PriFi automates the first steps of a procedure for developing general markers serving as common anchor loci across species.
  • To accommodate users with special preferences, configuration settings and criteria can be customized.
Keywords:
  • PCR
  • Polymerase Chain Reaction
  • PCR primer designing tool
  • DNA primers
  • degenerate primers designing tool
  • DNA sequence alignment
  • multiple sequence alignment
This record last updated: 11-07-2005
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