MCB 247 Homepage, Spring 2009.

Genome Project Laboratory

Instructors: Rachel Brem, Michael Eisen, Lior Pachter

Lectures: Tuesdays and Thursdays, 1:00pm-5:00pm in 2032/2038 VLSB.
Course Control Number: 59713

Links

Illumina Genome Analyzer System
BioPerl
Unix introduction and quick reference
VI tutorial
Emacs tutorial

Slides

Sequence assembly
Gene finding
Read mapping with Bowtie

References

A. Fleming: On the antibacterial action of cultures of a Penicillum, with special reference to their use in the isolation of B. influenzae
M.A. van den Berg et al.: Genome sequencing and analysis of the filamentous fungus Penicillum chrysogenum

Software

Velvet sequence assembler
BowTie read mapper
SNAP gene finder, ZFF format
Exonerate alignment and gene prediction.
JIGSAW annotation system