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Bioinformatics for the Canadian Potato Genome Project

Bioinformatics for the Canadian Potato Genome Project. David De Koeyer, Martin Lagü e and Rebecca Griffiths Wageningen September 18, 2004. Canadian Potato Genome Project. Research Areas. Genomics Operations: EST sequence generation (100,000). Expression Analysis: Microarray profiling.

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Bioinformatics for the Canadian Potato Genome Project

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  1. Bioinformaticsfor the Canadian Potato Genome Project • David De Koeyer, Martin Lagüe and Rebecca Griffiths • Wageningen September 18, 2004

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

  3. Router DMZ Firewall AAFC Internet

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

  5. 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).

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

  7. Bioinformatics Interests: • Potato Genome Sequencing • Comparative genomics / mapping • Marker development • Gene expression profiling

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