iGAP: Integrative Grid-enabled Genome Annotation Pipeline

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Presentation transcript:

iGAP: Integrative Grid-enabled Genome Annotation Pipeline Wilfred Li, Ph.D. Integrative Biosciences Program San Diego Supercomputer Center University of California, San Diego http://eol.sdsc.edu

Encyclopedia Of Life Project High quality functional and 3-D structure assignment using iGAP Grid-enabled bioinformatics applications Optimization Dedicated and grid resources Integrative biological data warehouse Web services consumer Distributed database and data mining Advanced query environment Open Notebook Web services provider

iGAP Workflow Reassemble proteome, Data replication PAT-NR Proteome 1000+ Genomes Proteome Specific Benchmarking iGAP: Prestaging Execution Monitoring Only unique sequences are processed DBMS iGAP WMS

Protein sequences Prediction of : NR, PFAM signal peptides (SignalP, PSORT) transmembrane (TMHMM, PSORT) coiled coils (COILS) low complexity regions (SEG) Structural assignment of domains by PSI-BLAST profiles on FOLDLIB Structural assignment of domains by 123D on FOLDLIB Structural assignment of domains by WU-BLAST Store assigned regions in the DB Functional assignment by PFAM, NR assignments SCOP, PDB FOLDLIB NR, PFAM Building FOLDLIB: PDB chains SCOP domains PDP domains CE matches PDB vs. SCOP 90% sequence non-identical minimum size 25 aa coverage (90%, gaps <30, ends<30) Domain location prediction by sequence structure info sequence info Step 1 Step 2 Step 3 Step 4 Step 5 Step 6

Workflow Management System for iGAP Grid Resources Work Stations Blue Horizon WMS SRB SDSC Others BII Japst Anywhere

EOL and APST The AppLeS Parameter Sweep Template (APST) provides EOL with transparent access to Grid resources and smart scheduling via Grid middleware. EOL Software/Data Grid Resources A P S T Globus GRAM/GASS SSH/SCP Application Description SRB/SFTP PBS/Loadleveler/Condor Grid Metadata Globus MDS/NWS/Ganglia

Acknowledgement SDSC Ceres Inc. BII, Singapore Fran Berman SDSC Director Philip E. Bourne IBS Director Mark Miller Project Coordinator Ilya N. Shindyalov CE Greg Quinn Web service Coleman Mosley Vicente Reyes Robert Byrnes Kim Baldrige iCC Director Jerry Greenberg CE portal Philip Papadoplous Rocks Mason Katz Greg Bruno SDSC Chaitan Baru David Archbell Jerry Rowley UCSD Peter Arzberger PRAGMA Henri Casanova Jim Hayes Ceres Inc. Nickolai Alexandrov 123D Richard Flavell BII, Singapore Larry Ang Kishore Sakharkar Arun Krishnan Atif Shahab Other BII members Everyone else Additional partner institutions