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Gene Curation - Future.

This document provides an overview of the advisory board meeting held at CSH in 2005, focusing on future directions in gene curation for C. elegans. Key topics discussed include the continuation of gene model curation, curation of new sequence features, and methods to improve gene prediction and annotation. Discussions also covered the use of third-party submissions, literature inputs, and the integration of sequence data from other nematodes. The meeting emphasized the need for collaboration, manual scanning of genomes, and addressing known gene problems in related species.

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Gene Curation - Future.

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  1. Gene Curation - Future. C.elegans???? Paul Davis The Sanger Institute Advisory Board Meeting , C.S.H. 2005

  2. Overview • Things we will continue to do. • Gene Model curation – future directions • Curation of new sequence features. • Possible features to curate • EMBL/GenBank sequence features. • Other nematodes. Advisory Board Meeting , C.S.H. 2005

  3. We Will Continue To Do. • C. elegans Sequence Changes. • Transcript Data. • 3rd Party Submissions. • C. elegans Gene Model curation. • mRNA/EST data from NDBs. • User input. • Literature. • Maintain current curation lists. Advisory Board Meeting , C.S.H. 2005

  4. Future Directions. • Investigate use of additional sequence features for gene prediction/annotation. • features • Protein alignments • WABA alignments – pairwise alignments • elegans::briggsae • Other nematode species. • SAGE tags • Clone boundaries and chromosome ends • Weak splice sites. • Short Introns. Advisory Board Meeting , C.S.H. 2005

  5. Future • Approaches • Manual scan • Drive scripted generation of new curation lists. Advisory Board Meeting , C.S.H. 2005

  6. Manual Scan. • Regions • 2 X 1Mb pilot sequences. • Each Mb pilot will be made of 5 sequence blocks of ~200kb. • Gene-rich internal regions • Chromosome arms. • Split between centre. • 2 centres to collaborate and QC. Advisory Board Meeting , C.S.H. 2005

  7. Scan Aims • Data resulting from the scan will • Identify new curation targets. • Potentially alter current curation strategy. • Timings • 1Mb. • Whole Genome. Advisory Board Meeting , C.S.H. 2005

  8. Caltech Literature Curators Sanger/St Louis Sequence Curators. Expanding Sequence Data. • Curation of new sequence features. • A start was made back in Dec 2004 • Manual annotation of 155 binding_site features taken from scientific literature. • Possible features to curate • Promoters defined experimentally in literature • EMBL/GenBank sequence features. Advisory Board Meeting , C.S.H. 2005

  9. Binding Site Features ceh-22 Advisory Board Meeting , C.S.H. 2005

  10. C. briggsae Gene Curation. • Agreed to start tackling known Gene problems • User community. • Data from the ~2500 briggsae ESTs. • User community expectations. • Is it good enough to have 1 well curated gene set for elegans, partial annotation on briggsae but only computationally derived gene sets for the other nematodes. Advisory Board Meeting , C.S.H. 2005

  11. Discussion Topics • Either refine elegans further or curate new genomes? • Curation of other nematode species • C. briggsae has ~2500 ESTs • C. remanei has ~15000 ESTs • Other elegans gene predictions • Inclusion of additional predicted gene sets. e.g.GeneMark.hmm – (Mark Borodovsky) • Or is it good enough having the curated elegans set and 2 additional gene sets. • Genefinder – (Phil Green) • Twinscan – (Michael Brent) Advisory Board Meeting , C.S.H. 2005

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