Comparative genome mapping

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Comparative genome mapping

• Todd Vision
• Department of Biology
• University of North Carolina at Chapel Hill

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(No Transcript)
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comparative maps
spaghetti diagram
crop circle
Gale Devos 1998 PNAS 951972
Livingstone et al 1999 Genetics 1521183
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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

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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
• tjv_at_bio.unc.edu
• 843-4507
• 102 Coker Hall