PolyMFind

Overview

PolyMFind is a program that scans through a multiple genome alignment to identify and classify all polymorphisms. The multiple sequence alignments are generated by Mauve. Since the alignment is generated using sequences stored in CoGe, PolyMFind can query the location of each polymorphism and identify any underlying genomic feature. If the genomic feature is a protein coding gene, the change in coding sequence is assessed to determine if it causes a frameshift, synonymous, or nonsynonymous mutation.

Note: There a several sources of errors for these polymorphisms that from three major factors:

• Sequencing errors
• Assembly errors
• Multiple sequence alignment errors

PolyMFind not only identifies and classifies polymorphisms, but also provides:

• A false positive score of the polymorphism to help prioritize ones to investigate further
• Views of data to assess whether a polymorphism is real
• Tools to compare genomic regions to assess whether a polymorphism is real
• Information about genes with polymorphisms
• Links to extract addition information for genes
• Summary tables of:
  • All polymorphisms detected
  • Polymorphisms detected in each genome
  • Number of polymorphisms that may be the result of a homopolymer sequences error
  • Counts of all the false positive scores