By Michael Han Sanger Wormbase Group SAB 2008 Comparative Genomics with.

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Presentation transcript:

by Michael Han Sanger Wormbase Group SAB 2008 Comparative Genomics with

SAB 2008 Overview Comparative Genomics in WormBase Orthology Synteny

SAB 2008 Divergence “closely related” means something different (wormbook.org 10/06)‏

SAB 2008 Orthology Data imported from external sources (TreeFam,EnsEMBL-Compara, Inparanoid, OMA) Created during the build process for nematodes (WormBase-Compara) created outside of the build process (KOGs / OrthoMCL) from user submission (e.g. LaDeanna Hillier)‏

SAB 2008 Ortholog Genes C. remanei C. elegans Human Mouse Fly C. bruggia 3864 C. remanei C. elegans Human Mouse Fly C. bruggia 3864 C. elegans B.malayiC.briggsae C.remanei H.sapiensM.musculus D.melanogaster

SAB 2008 Usage flag gene models for curation projecting Worm Gene Names adding external crossreferences human disease orthologs (OMIM)‏ non-WormBase orthologs

SAB 2008 Gene Model 1:2 M:N 1:1 Orphan 1:1 Split Gene ? 1:1 missed gene ?

SAB 2008 WormBase-Compara Ensembl-core databases C.elegans / C.briggsae / C.remanei / C.brenneri / B.malayi Ensembl-compara databases 1. Orthology II. Synteny Ensembl-Hive Job Management on LSF (about 8 hours for 5 species)‏ AceDB build database synchronisation Blast / Protein Annotation /Repeats Orthologs Orthology 1. all vs all blast (proteins)‏ 2. linkage clustering 3. Protein alignments (MUSCLE)‏ 4. Tree building (PHYML)‏ 5. dN/dS (CODEML)‏ Synteny 1. all vs all blast (exons)‏ 2. synteny (MERCATOR)‏ 3. alignments (PECAN)‏ (4. conserved elements)‏

SAB 2008 WormBase-Compara uses the Ensembl-compara code from EBI/Ensembl 5(7) internal Ensembl core / 2 compara databases Nematode orthologs assigned to 17,443 of 20,177 (~87%) coding C.elegans genes (WS190)‏ Whole Genome Alignments synteny blocks MERCATOR 4-genome alignments PECAN

SAB 2008 Synteny Data WABA pairwise alignments MERCATOR synteny blocks PECAN multi-genome alignments

SAB 2008 PECAN

SAB 2008 Viewers web display GBrowse tracks alignments

SAB 2008 (Near) Future add new genesets for new species (parasitic nematodes)‏ try whole genome alignments with more distant species (Heterorhabditis / Brugia / Pristionchus)‏ unified TreeFam / Compara improved QC on ortholog relationships additional paralog information

SAB 2008 Aknowledgements Sanger: Avril Coghlan (Treefam / NGASP)‏ Heng Li (TreeFam)‏ Ed Griffith (AceDB)‏EBI: Javier Herrero and Albert Viella (Compara)‏ Patrick Meindel and Andreas Kahari (stableid_mapping)WashU: LaDeanna Hillier (C.briggsae orthologs)‏ Eidgenössische Technische Hochschule Zürich (ETH): Adrian Schneider (OMA)‏ Stockholm Bioinformatics Center (SBC): Gabriel Östlund (Inparanoid)‏