Transcript Fast identification and statistical evaluation of

Comparative genome mapping
Todd Vision
Department of Biology
University of North Carolina at Chapel Hill
8/22/03 CS RA fair
8/22/03 CS RA fair
comparative maps
spaghetti diagram
crop circle
Gale & Devos 1998 PNAS 95:1972
Livingstone et al 1999 Genetics 152:1183
8/22/03 CS RA fair
applications
Kohn MH, Pelz HJ. (2000) Blood 96(5):1996-8.
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Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121
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FISH v1.0:
Fast Identification of Segmental Homology
• Identification of related chromosomal segments
– Dynamic programming: speed and optimality guarantee
– Generalization to multiple alignments
– Few parameters are required (e.g. T)
• Statistical assessment
– Null model of duplication and transposition
– Analytic p-values (i.e. no permutation testing)
• http://www.bio.unc.edu/faculty/vision/lab/FISH
– for source code, compiled executables, documentation, sample
data
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eAssembler
• The goal is to reconstruct
‘true’ or ‘ancestral’ gene
order by joining duplicated
segments with overlapping
gene content
• Reconstructed gene order
should allow improved
prediction of gene content in
unsequenced genomes
• With Luke Huan, Jan Prins,
Wei Wang
8/22/03
CS13,
RA137-144.
fair
Blanc, Hokamp, Wolfe (2003) Genome
Res.
PHYTOME
integrating plant genome maps,
sequences and phylogenies
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Mapping genes underlying speciation
• Mimulus lewisii and cardinalis
• Isolated by pollinators and by
habitat
• Two major genes underlying
differences in pollinator
syndrome have been mapped
to chromosomal segments
• But their functions (and
evolutionary history) are
currently unknown
• We are using comparative
genomics to isolate these
genes
8/22/03 CS RA fair
Research assistant wanted
• To help implement a pipeline for
sequence analysis that ties together
existing bioinformatic tools
Mimulus
Sequence
data
BLAST
ClustalW
Genbank
Sequence
data
8/22/03 CS RA fair
Primer3
Experiments
Qualifications
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OOP in Perl
Regular expressions
UNIX shell
RDMS (MySQL)
Willingness to learn a little genetics
Willingness to work as a team
• Interested? More questions?
Todd Vision
[email protected]
843-4507
102 Coker Hall
8/22/03 CS RA fair