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Internet tools for genomic analysis

Internet tools for genomic analysis. June 22, 2006 dwildman@med.wayne.edu 577-8234. Overview. Lecture types of data important information in records Sources of error Demo NCBI, UCSC, ENSEMBL, GNF atlas Exercises. Sequences + SantaCruz genome.ucsc.edu NCBI Trace archives Genbank

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Internet tools for genomic analysis

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  1. Internet tools for genomic analysis June 22, 2006 dwildman@med.wayne.edu 577-8234

  2. Overview • Lecture • types of data • important information in records • Sources of error • Demo • NCBI, UCSC, ENSEMBL, GNF atlas • Exercises

  3. Sequences + SantaCruz genome.ucsc.edu NCBI Trace archives Genbank Ensembl HapMap Expression Symatlas.org Stanford MicoArray database Annotation geneontolgy.org Panther pantherdb.org Affymetrix Important genomic databases

  4. Data Quality • Raw • Curated • Transformed

  5. Data Types • Sequences • Protein vs. DNA • WGS • BACs • NR • CDs • partial reads • Coverage • RefSeqs • ESTs

  6. WIRED magazine: June 2006

  7. WIRED magazine: June 2006

  8. WIRED magazine: June 2006

  9. NCBI Databases • Taxonomy • Nucleotide • Conserved domains • SNP • Trace Archives

  10. Mammalian Diversity • ~5400 living species • 29 Orders Wilson & Reeder 2005

  11. NCBI Databases • Taxonomy • Tax Browser • [orgn] • Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information. • Nucleotide • Conserved domains • SNP • Trace Archives

  12. NCBI Databases • Taxonomy • Nucleotide • Core nucleotide • RefSeq • EST • BLAST • example:leptin • Conserved domains • SNP • Trace Archives

  13. NCBI Databases • Taxonomy • Nucleotide • Conserved domains • http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml • Example TLR2 • NP_003255 • CDART: Conserved Domain Architecture Retrieval Tool • SNP • Trace Archives

  14. NCBI Databases • Taxonomy • Nucleotide • Conserved domains • SNP • Example COX5A • nsSNPcounter • http://homopan.wayne.edu/ • Trace Archives

  15. NCBI Databases • Taxonomy • Nucleotide • Conserved domains • SNP • Trace Archives

  16. The UCSC Genome browser: http://genome.ucsc.edu

  17. Santa Cruz • Tracks • BLAT • Conservation • Discovery

  18. The UCSC Genome browser: chromosome 19: 63,811,651 bp. Human Mar 2006 Assembly

  19. The Human b Hemoglobin Gene Cluster http://genome.ucsc.edu

  20. Endoglin expression

  21. Endoglin conservation

  22. GNF SYMATLAS • http://symatlas.gnf.org/SymAtlas/ • Example: ?

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