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[Molecular-evolution] Panseq - genomic comparison software

kropinsk from queensu.ca via mol-evol%40net.bio.net (by kropinsk from queensu.ca)
Tue Aug 17 09:04:08 EST 2010


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Panseq (http://76.70.11.198/claing/panseq/panseq_home.cgi)
- a group of tools, developed by Chad Laing (Public Health Agency of Canada)  for
the analysis of the 'pan genome' of a group of genomic sequences. The
pan-genome of a bacterial species consists of a core genome and an accessory
gene pool, the latter of which allows subpopulations of the organism to adapt
to specific environments. These include “Novel Region Finder”, which will find
sequences that are unique to a strain or group of strains with respect to
another strain or group of strains. “Core/Accessory Genome Analysis” will
define the core and accessory genome of a group of strains, based on the user
configurable parameters of region size and percent sequence identity. Outputs
of this feature include concatenated core genomes for each sequence examined, a
tab-delimited table depicting the presence / absence of each accessory region
among all the sequences examined, a tab-delimited table depicting each SNP
among all the sequences examined and NEXUS format files of both the core and
accessory genome. “Loci Selector” determines the most variable and
discriminatory loci from a group. 

 

This site can also
be accessed at: http//molbiol-tools.ca/Genomics.htm



Andrew M. Kropinski
Research Scientist & Program Lead, Host & Pathogen Determinants, Laboratory for Foodborne Zoonoses
Adjunct Professor , Microbiology & Immunology, Queen's University
Adjunct Professor, Molecular & Cellular Biology, University of Guelph

URL: Online Analysis Tools (http://molbiol-tools.ca)


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