8/22/03 CS RA fair Comparative genome mapping Todd Vision Department of Biology University of North Carolina at Chapel Hill
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):
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) –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 Blanc, Hokamp, Wolfe (2003) Genome Res. 13,
8/22/03 CS RA fair 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 BLAST Mimulus Sequence data Genbank Sequence data ClustalWPrimer3 Experiments
8/22/03 CS RA fair 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 Coker Hall