comparative genome mapping
DESCRIPTION
Comparative genome mapping. Todd Vision Department of Biology University of North Carolina at Chapel Hill. comparative maps . spaghetti diagram. crop circle. Gale & Devos 1998 PNAS 95:1972. Livingstone et al 1999 Genetics 152:1183. applications. - PowerPoint PPT PresentationTRANSCRIPT
8/22/03 CS RA fair
Comparative genome mapping
Todd VisionDepartment 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
Livingstone et al 1999 Genetics 152:1183 Gale & Devos 1998 PNAS 95:1972
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
Blanc, Hokamp, Wolfe (2003) Genome Res. 13, 137-144.
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PHYTOMEintegrating 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
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Research assistant wanted• To help implement a pipeline for
sequence analysis that ties together existing bioinformatic tools
BLAST
MimulusSequence
data
GenbankSequence
data
ClustalW Primer3 Experiments
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Qualifications• 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
102 Coker Hall