Bioinformatics for the Canadian Potato Genome Project David De Koeyer, Martin Lagüe and Rebecca Griffiths Wageningen September 18, 2004.

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Presentation transcript:

Bioinformatics for the Canadian Potato Genome Project David De Koeyer, Martin Lagüe and Rebecca Griffiths Wageningen September 18, 2004

Research Areas Genomics Operations: EST sequence generation (100,000) Expression Analysis: Microarray profiling Potato Mutant Population Generation: Activation tagged lines (10,000 lines) Canadian Potato Genome Project

Internet DMZ Firewall Router AAFC

MySQL Web Browser Web Server (Apache) HTML JavaScript JAVA applets PHP (PHPGroupWare) Perl (bioPerl) Applications (ex: Blast) bioGW modules: Query (database) Blast (database) Blast (application) Contig (database) LIMS (database) Viewers: Artemis bcmTraceViewer JalView

Canadian Bioinformatics Resources CBR membership gives CPGP users enhanced access to CBR tools and services. This includes access to specialized bioinformatics software, enhanced computing power (BLAST Cluster).

Tracefiles Base calling using Phred EST sequences in fasta format Clean EST sequences; all adapter and vector sequences removed Crossmatch And perl scripts Raw Sequence DataProcessing Sequence DataSequence Data Assembly Sequence Annotation Quality trim sequences (threshold 10) Cluster Assemble 94 % Similarity Remove contaminants Ecoli contaminants Mitochondrial contaminants Chloroplast contaminants rRNA, snoRNA Minimum length filter (100 bp) Temporarily Mask: Solanum repeats Poly A tails Low-complexity regions Blast Paracel Transcript Assembler Annotation Data Acquisition Tool Tmap Pfam Prosite Signalcleave TraceScan Autonomous Annotation Process

Bioinformatics Interests: - Potato Genome Sequencing - Comparative genomics / mapping - Marker development - Gene expression profiling