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Bioinformatics for the Canadian Potato Genome Project David De Koeyer, Martin Lagüe and Rebecca Griffiths Wageningen September 18, 2004
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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
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Internet DMZ Firewall Router AAFC
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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
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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).
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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
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Bioinformatics Interests: - Potato Genome Sequencing - Comparative genomics / mapping - Marker development - Gene expression profiling
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