Oral Session
S5 Genome
January 22, Thursday
Morning session (09:00〜12:15)
S5-01〜S5-07
Chairperson:
Prof. S. FITZ-GIBBON
Prof. N. OGASAWARA
Integrated Analysis of Whole Genomes: Automated VS. Assisted Decisions
Terry GAASTERLAND*
Areonne National Laboratory /Universitv of Chicago, Chicago, IL. U.S.A.
(This talk includes work done in collaboration with Christoph Sensen, Paul Gordon and Mark Ragan of the Institute for Marine Biosciences, Halifax, Nova Scotia)
Annotating thousands of ORFs in a newly sequenced genome is a detailed process that involves assessing evidence of different types from many sources. We have built a system called MAGPIE, to find coding regions, collect evidence to answer "Does it code?" and "For what?", and then facilitate confirmation and editing of annotations. Through MAGPIE, we have been exploring how to automate the annotation process, make decisions automatically, assist the user in making final annotations, and update annotations regularly.
We illustrate the steps and difficulties involved in annotation with four cases:
an ORF with "perfect" evidence in which all tools agree
an ORF with strong evidence that is sparse but clear
an ORF with good but seemingly conflicting evidence
an ORF with strong, partial evidence that covers half of the ORF
an ORF with weak evidence
Finally, the talk will touch on other uses of MAGPIE, namely, cross-genome comparisons, tracking random protein sequences, and comparing microbial pathogens to eukaryotes.
