[Bio-software] Panseq - genomic comparison software

kropinsk from queensu.ca via bio-soft%40net.bio.net (by kropinsk from queensu.ca)
Tue Aug 17 08:58:39 EST 2010


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Panseq (http=3A//76=2E70=2E11=2E198/claing/panseq/panseq=5Fhome=2Ecgi)
- a group of tools=2C developed by Chad Laing (Public Health Agency of C=
anada)=2C=A0 for
the analysis of the =27pan genome=27 of a group of genomic sequences=2E =
The
pan-genome of a bacterial species consists of a core genome and an acces=
sory
gene pool=2C the latter of which allows subpopulations of the organism t=
o adapt
to specific environments=2E These include =93Novel Region Finder=94=2C w=
hich will find
sequences that are unique to a strain or group of strains with respect t=
o
another strain or group of strains=2E =93Core/Accessory Genome Analysis=94=
 will
define the core and accessory genome of a group of strains=2C based on t=
he user
configurable parameters of region size and percent sequence identity=2E =
Outputs
of this feature include concatenated core genomes for each sequence exam=
ined=2C a
tab-delimited table depicting the presence / absence of each accessory r=
egion
among all the sequences examined=2C a tab-delimited table depicting each=
 SNP
among all the sequences examined and NEXUS format files of both the core=
 and
accessory genome=2E =93Loci Selector=94 determines the most variable and=

discriminatory loci from a group=2E=A0

=A0

This site can also
be accessed at=3A http//molbiol-tools=2Eca/genomics=2Ehtml



Andrew M=2E Kropinski
Research Scientist =26 Program Lead=2C Host =26 Pathogen Determinants=2C=
 Laboratory for Foodborne Zoonoses
Adjunct Professor =2C Microbiology =26 Immunology=2C Queen=27s Universit=
y
Adjunct Professor=2C Molecular =26 Cellular Biology=2C University of Gue=
lph

URL=3A Online Analysis Tools (http=3A//molbiol-tools=2Eca)




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