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Comparative genome mapping

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.

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Comparative genome mapping

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

  2. 8/22/03 CS RA fair

  3. 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

  4. applications Kohn MH, Pelz HJ. (2000) Blood 96(5):1996-8. 8/22/03 CS RA fair

  5. Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121 8/22/03 CS RA fair

  6. 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 8/22/03 CS RA fair

  7. 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. 8/22/03 CS RA fair

  8. PHYTOMEintegrating plant genome maps, sequences and phylogenies 8/22/03 CS RA fair

  9. 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

  10. Mimulus Sequence data BLAST ClustalW Primer3 Experiments Genbank Sequence data Research assistant wanted • To help implement a pipeline for sequence analysis that ties together existing bioinformatic tools 8/22/03 CS RA fair

  11. 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 tjv@bio.unc.edu 843-4507 102 Coker Hall 8/22/03 CS RA fair

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