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Introduction to BioComputing Biology in silico 3 rd February 2010

Introduction to BioComputing Biology in silico 3 rd February 2010. Carrie Iwema , PhD, MLS Molecular Biology Information Specialist Health Sciences Library System University of Pittsburgh iwema@pitt.edu http://www.hsls.pitt.edu/guides/genetics. General Topics. Information Overload

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Introduction to BioComputing Biology in silico 3 rd February 2010

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  1. Introduction to BioComputingBiology in silico3rd February 2010 Carrie Iwema, PhD, MLS Molecular Biology Information Specialist Health Sciences Library System University of Pittsburgh iwema@pitt.edu http://www.hsls.pitt.edu/guides/genetics

  2. General Topics • Information Overload • Genome  Gene  Protein http://www.hsls.pitt.edu/guides/genetics

  3. Specific Topics • Information Overload • PubMed • Alternatives to PubMed • GoPubMed • Novoseek • PubGet • Molecular Databases • HSLS Molecular Biology Information Service • Genome  Gene Protein • Genome Biology • Genome Browsers • UCSC Genome Browser • NCBI MapViewer • EntrezGene • UniProt http://www.hsls.pitt.edu/guides/genetics

  4. Information Overload 5,394 Journals 1.3 billion searches in 2009 • STAT1 http://www.hsls.pitt.edu/guides/genetics

  5. Alternatives to PubMed http://www.hsls.pitt.edu/guides/genetics

  6. Growth of Molecular Databases 2010: 1230 2009: 1170 2008: 1075 Source: Nodal Point Blog http://www.hsls.pitt.edu/guides/genetics

  7. Molecular Databases • Nucleic Acids Research: Oxford Journals • Annual Database Issue • Annual Web Server Issue • Journals • Bioinformatics: Oxford Journals • BMC Bioinformatics: BioMed Central • Database: Oxford Journals *new in 2009* • Articles on “genetic databases” • PubMed: 21,851 results • MeSH: 16,398 results http://www.hsls.pitt.edu/guides/genetics

  8. HSLS Molecular Biology Information Service http://www.hsls.pitt.edu/guides/genetics

  9. HSLS OBRC http://www.hsls.pitt.edu/guides/genetics

  10. HSLS OBRC in Science http://www.hsls.pitt.edu/guides/genetics

  11. search.HSLS.MolBio • Integrated search system • Databases & Software • Articles on Databases & Software • Genes/Proteins • Pathways • Protocols • Videos • Recommended Articles • Tabbed browsing • Clustered search results http://www.hsls.pitt.edu/guides/genetics

  12. Hands-on exercises • Locate databases on • Natural antisense, UTR, copy number variation • Retrieve gene information for • Your favorite gene, BRCA1, STAT1 • Find a suitable protocol for • Methylation PCR, in situ hybridization, primer design • Identify videos on • Protein structure prediction, human genome project http://www.hsls.pitt.edu/guides/genetics

  13. Genome Biology http://www.hsls.pitt.edu/guides/genetics

  14. From Cell to Gene Human Genome Project Video http://www.hsls.pitt.edu/guides/genetics

  15. Genome Biology Time Line RNA Bacteriophage MS2 Human Genome Draft Seq Diploid Genome seq of an Individual Human 1976 2001 2007 2010 1995 2003 2008 Haemophilus Influenza Published Complete Human Ref Genome Published Complete Genomes: 1191 organisms Jim Watson Genome Human Genome Project Video http://www.hsls.pitt.edu/guides/genetics

  16. Genome Resources • NCBI: • Genomes Resources : Link • Genome Project • Genome: 6108 species • Genomes OnLine Database (GOLD): Link • JGI: Integrated Microbial Genomes: Link http://www.hsls.pitt.edu/guides/genetics

  17. NCBI Genome Resources http://www.hsls.pitt.edu/guides/genetics

  18. Practice Question: • Query:  Check the status of genome sequencing for an organism, such as rabbit. • Answer: • Pick an organism or metagenome project name. • Search the Genome Project database. To get the most precise results specify the organism field when searching with an organism name, for example: human[orgn]. • Click on the desired Genome Project if more than one result. • The Genome Project summary page will provide information of available projects and sequencing status. http://www.hsls.pitt.edu/guides/genetics

  19. NCBI Genome Project • A collection of complete and in-progress large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals for browsing and retrieving projects pertaining to each organism. Rabbit CLICK http://www.hsls.pitt.edu/guides/genetics

  20. NCBI Genome Project : Rabbit Genome http://www.hsls.pitt.edu/guides/genetics

  21. NCBI Genome Project : Rabbit Genome http://www.hsls.pitt.edu/guides/genetics

  22. NCBI Entrez Genome: http://www.hsls.pitt.edu/guides/genetics

  23. Genomes Online Database (GOLD) • http://genomesonline.org/index2.htm • Global resource for comprehensive access to information regarding complete and ongoing genome projects, metagenomes, and metadata. “genome sequencing has come of age, and genomics will become central to microbiology's future. It may appear at the moment that the human genome is the main focus and primary goal of genome sequencing, but do not be deceived. The real justification in the long run, is microbial genomics” Carl Woese, 1998 http://www.hsls.pitt.edu/guides/genetics

  24. Genome Browsers http://www.hsls.pitt.edu/guides/genetics

  25. Genome Browsers: What are they? Genome Browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. http://www.hsls.pitt.edu/guides/genetics

  26. Genome Browsers Display: Vertical • The Big Three • NCBI MapViewer • UCSC Genome Browser • EBI Ensembl • Generic Genome Browser (Gbrowse) • JBrowse(Ajax based like Google Map) Display: Horizontal http://www.hsls.pitt.edu/guides/genetics

  27. Tutorial Articles Link Link Link Link http://www.hsls.pitt.edu/guides/genetics

  28. Tutorial/Seminar Videos Link Link Link Link http://www.hsls.pitt.edu/guides/genetics

  29. UCSC Genome Browser http://www.hsls.pitt.edu/guides/genetics

  30. Navigating the Human Genome Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 UCSC Genome Browser http://www.hsls.pitt.edu/guides/genetics

  31. UCSC Genome Browser: navigating a genomic region Set up basic browser parameters http://www.hsls.pitt.edu/guides/genetics

  32. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  33. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  34. UCSC Genome Browser: navigating a genomic region Start fresh http://www.hsls.pitt.edu/guides/genetics

  35. UCSC Genome Browser: navigating a genomic region Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 What genes are present in this region? http://www.hsls.pitt.edu/guides/genetics

  36. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  37. NCBI sequence databases • RefSeq • based on GenBank records; non-redundant, expert-verified databases of reference sequences Link • GenBank • archival database of nucleotide sequences from >160,000 organisms Link http://www.hsls.pitt.edu/guides/genetics

  38. International Nucleotide Sequence Database Collaboration http://www.hsls.pitt.edu/guides/genetics

  39. Primary Vs Derivative databases http://www.hsls.pitt.edu/guides/genetics

  40. RefSeq Scope & Accessions • Genomic DNA • NC_123456 - complete genome, chromosome, plasmid • NG_123456 - genomic region • NT_123456 - genomic contig • mRNA NM_123456 • Protein NP_123456 more about RefSeq scope and accessions... http://www.hsls.pitt.edu/guides/genetics

  41. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  42. UCSC Genome Browser: navigating a genomic region Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 Zoom in and display only the EGFR gene http://www.hsls.pitt.edu/guides/genetics

  43. UCSC Genome Browser: navigating a genomic region Select the gene region from the “Scale” track to zoom in http://www.hsls.pitt.edu/guides/genetics

  44. UCSC Genome Browser: navigating a genomic region Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 Display all Single Nucleotide polymorphisms (SNPs) present in this gene http://www.hsls.pitt.edu/guides/genetics

  45. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  46. UCSC Genome Browser: navigating a genomic region Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 Retrieve the nucleotide sequence of this genomic region showing all exons in blue and SNPs in Red, bold faced and underlined. http://www.hsls.pitt.edu/guides/genetics

  47. UCSC Genome Browser: navigating a genomic region http://www.hsls.pitt.edu/guides/genetics

  48. UCSC Genome Browser: navigating a genomic region: sequence view http://www.hsls.pitt.edu/guides/genetics

  49. UCSC Genome Browser: navigating a genomic region Browse the region of human chromosome 7 between bp54,318,043 to 55,974,438 Look in probable promoter region and see if there’s anything interesting… http://www.hsls.pitt.edu/guides/genetics

  50. UCSC Genome Browser: navigating a genomic region Zoom out http://www.hsls.pitt.edu/guides/genetics

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