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
Literature & Tutorials:
This record last updated: 11-07-2005