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