05/04/2005

Informatics Meeting

C. elegans C. elegans – “Back To The – “Back To The Future”. Future”.

Paul Davis (aka Huey)

05/04/2005

Informatics Meeting

OverviewOverview≈ C. elegans Gene Prediction

≈ Past.≈ Overview of genome project.≈ 1st Pass annotation

≈ Present.≈ Script based list generation.

≈ Gene Refinement (Transcript Based).≈ Small peptides.

≈ C. briggsae comparison.≈ Large external gene family analysis.

≈ Future.≈ Un-annotated Overlap between gene predictors≈ Gene Family curation.≈ Multiple species comparison.

≈ Summary.

05/04/2005

Informatics Meeting

PastPast≈ Genome Project

≈ C. elegans 1st multicellular organism genome published 1998.

≈ 97-Mb of sequence made up of ≈ 2527 cosmids, ≈ 257 YACs,≈ 113 fosmids,≈ 44 PCR products.

≈ 5 gaps closed by 2002.≈ Annotated to find 19,099 protein coding genes.

≈ 1st pass annotation Genefinder (Phil Green WASHU).

≈ Curators appraised gene predictions on a clone by clone basis as they were finished.

05/04/2005

Informatics Meeting

Genome ViewGenome View

PredictedPartially Confirmed Confirmed

Colour corresponds to strand not confidence.

05/04/2005

Informatics Meeting

Stats for WS141Stats for WS141

≈ Currently 22,436 gene predictions.≈ 11,169 “un-touched”

≈ + good 1st pass annotation.≈ + re-annotated >50%.

≈ 2,576 Confirmed status.≈ Unlikely to change.

≈ 5,624 Partially Confirmed.≈ Potentially modified.

≈ 2,969 Predicted.≈ Potentially removed or altered.

05/04/2005

Informatics Meeting

PresentPresent(re)annotation of a genome(re)annotation of a genome

Painting by numbers

Painting the Forth Rail Bridge

05/04/2005

Informatics Meeting

(re)annotating a genome(re)annotating a genome≈ We adopted a ‘paint by numbers’ approach involving

automated appraisal of all gene models on a regular basis.≈ Generation of lists of genes/features to be checked by

human annotators.

Appraise Curate

Process and report

Release and synchronise

05/04/2005

Informatics Meeting

Script Based Targeted Script Based Targeted AnnotationAnnotation

≈ Create a number of curation lists≈ Confirmed introns not in gene models≈ ESTs/mRNAs in introns.≈ Overlapping Gene predictions.≈ Predictions overlapping known repeats.≈ Short Genes <150bp≈ Short introns <40bp

05/04/2005

Informatics Meeting

Transcript Based RefinementsTranscript Based Refinements

≈ Automatic import of transcript data during our build cycle.≈ C. elegans mRNAs/cDNAs.≈ C. elegans ESTs. ≈ Nematode ESTs.

≈ Processed and aligned to genome.≈ This produces data for our curation lists

05/04/2005

Informatics Meeting

Gene Refinement Fmap ViewGene Refinement Fmap View

≈ EST data points to 5’ extension and 3’ extension.

≈ Identified due to confirmed introns not in a gene model

5’

3’

Transcript Data

Refined Prediction

Old prediction

Confirmed intron.

05/04/2005

Informatics Meeting

Not all <150bp Predictions are Not all <150bp Predictions are Bad?Bad?

≈ Small peptides can be real.≈ H12D21.1 is a 34 aa peptide that appeared

on curation list.≈ Investigated.≈ Prediction had peptide similarity to 2 other

elegans proteins.≈ Multi sequence alignment proved

interesting.

05/04/2005

Informatics Meeting

H12D21.1 + Homols H12D21.1 + Homols Fmap View & M.S.A.Fmap View & M.S.A.

SignalP cleavage site

Gene Prediction

Protein Homology Blocks

05/04/2005

Informatics Meeting

New Family MembersNew Family Members

≈ Used tBlastn to identify other regions in genome,≈ Annotated these ORFs to give.≈ 9 additional family members≈ These have been called nspa-1 to 12

≈ Nematode Specific Peptide family A

Pseudogene

Expanded Family

05/04/2005

Informatics Meeting

C. briggsae C. briggsae ComparisonComparison

≈ C. elegans vs C. briggsae≈ C. briggsae hybrid gene set analysis (Avril Coghlan).

≈ Detailed in PloS Biol 2003 1:166-192 “The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.”

≈ WormBase Has worked to incorporate the ~1300 new genes reported.

05/04/2005

Informatics Meeting

Coding Gene Predictions Over Time.Coding Gene Predictions Over Time.

Increase in CDS due to 1st round of new genes identified by comparison with briggsae.

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Release

Number

PredictionsIncluding Isoforms

Coding Genes

briggsae hybrid gene set

05/04/2005

Informatics Meeting

Large family analysisLarge family analysis

≈ Worm Community Members.≈ Multi Sequence Alignments of some

large Families.≈ 7 TM receptor families

≈ 1700 family members≈ Sub families have been worked on by multiple

worm community members.≈ Hugh Robertson (University of Illinois)≈ Jim Thomas (University of Washington Seattle)≈ Jack Chen (CSH Laboratories)

05/04/2005

Informatics Meeting

FutureFuture

≈ Identify new avenues for gene refinement and identification.

≈ Looking at predictor overlaps≈ (Genefinder/Twinscan overlaps) vs

(WormBase Gene set)

≈ In house protein family analysis≈ Multiple species comparisons

05/04/2005

Informatics Meeting

Predictor Overlaps.Predictor Overlaps.

GenefinderPrediction

TwinscanPrediction

New CDS Prediction

Strong Splicing

Good briggsae DNA::DNA Alignment

05/04/2005

Informatics Meeting

Gene Family AnalysisGene Family Analysis

≈ Protein alignments of multiple family members can refine gene predictions.≈ ClustalW≈ blast≈ Main problems identified

≈ Incorrect splicing≈ Truncations≈ Invalid extensions

05/04/2005

Informatics Meeting

Example of a Small Family Example of a Small Family Analysis.Analysis.

≈ Problematic alignment≈ F56H6.9 appears to have 18aa extra sequence.≈ E03H4.4 seems to be lacking sequence.

05/04/2005

Informatics Meeting

Fmap View of F56H6.9Fmap View of F56H6.9

05/04/2005

Informatics Meeting

Example of Problem.Example of Problem.

≈ Problematic alignment

≈ Alignment following annotation.

05/04/2005

Informatics Meeting

Multiple Species Comparison.Multiple Species Comparison.≈ More nematode genomes are on their way

≈ C. remanei≈ shotgun in progress

≈ Blast server available http://genome.wustl.edu/projects/cremanei/

≈ PB2801≈ shotgun in progress

≈ C. japonica ≈ shotgun in progress

05/04/2005

Informatics Meeting

elegans/briggsae/remaneielegans/briggsae/remanei Alignment for nspa- like peptides.Alignment for nspa- like peptides.

05/04/2005

Informatics Meeting

SummarySummary

≈ Gene (Re)annotation >7 years.≈ New genes are still being discovered.

≈ Primarily Transcript driven.≈ More work on protein families≈ New strategies for gene prediction and

refinement.≈ Using multiple gene predictors≈ Multi species comparison

05/04/2005

Informatics Meeting

AcknowledgementsAcknowledgements≈ Genome Sequencing Center St. Louis

≈ Sequencing and finishing teams etc.

≈ WormBase team

Tamberlyn Bieri Darin Blasiar

Phil Ozersky John Spieth

≈ Wellcome Trust Sanger Institute ≈ Sequencing and finishing teams etc.

≈ WormBase team

Richard Durbin Anthony Rogers

Dan Lawson Mary Ann Tuli

≈ AceDB Ed Griffiths Roy Storey