Comparative genome mapping
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8/22/03 CS RA fair Comparative genome mapping Todd Vision Department of Biology University of North Carolina at Chapel Hill
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 Presentation
Transcript of Comparative genome mapping
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
