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Professional Development Course 1 – Molecular Medicine Genome Biology June 12, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services.

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Presentation on theme: "Professional Development Course 1 – Molecular Medicine Genome Biology June 12, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services."— Presentation transcript:

1 Professional Development Course 1 – Molecular Medicine Genome Biology June 12, 2012 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

2 Genomic achievements since the Human Genome Project http://www.hsls.pitt.edu/molbio

3 Objective Organism Whole Genome Sequence Databases Genome Browsers http://www.hsls.pitt.edu/molbio

4 Topics  Genome Sequencing Projects  NCBI Genome resources  Integrated Microbial Genome  UCSC Genome Bioinformatics  Genome Browsers  UCSC Genome Browser  UCSC Table Browser  NCBI Map viewer  Generic Genome Browser (Gbrowse) http://www.hsls.pitt.edu/molbio

5 Genome Biology Human Genome Project Video http://www.hsls.pitt.edu/molbio

6 Chromosome Structure http://www.hsls.pitt.edu/molbio

7 Genome Biology: Karyotype Adapted from NGHRI Trisomy 21 Monosomy X http://www.hsls.pitt.edu/molbio

8 Genome Biology: Karyotype NHGRI http://www.hsls.pitt.edu/molbio

9 Genome Biology: Molecular Cloning p53 CFTRNFkB 8 September, 1989 http://www.hsls.pitt.edu/molbio

10 Genome Biology : Time Line 1976 RNA Bacteriophage MS2 2001 Human Genome Draft Seq 2003 Published Complete Human Ref Genome 2007 Diploid Genome seq of an Individual Human 2011 Published Complete Genomes: 1863 organisms 1995 Haemophilus Influenza 2008 Jim Watson Genome Yeast 1996 1998 C. elegans 2002 Drosophila http://www.hsls.pitt.edu/molbio

11 DNA Sequencing Cost http://www.hsls.pitt.edu/molbio

12 Oxford Nanopore A 20-node installation, using 8,000-nanopore cartridges, is expected to deliver a complete human genome at 50- fold coverage in 15 minutes, according to the company, or 3 terabases of data per day, based on a sequencing speed of 300 bases per second. For that setup, the cost per gigabase is expected to be under $10. http://www.hsls.pitt.edu/molbio

13 Organism Whole Genome Sequences 20012012 http://www.hsls.pitt.edu/molbio

14 Organism Whole Genome Sequences Human Mouse Rat Dog Cow Chimp Rabbit …….. http://www.hsls.pitt.edu/molbio

15 Genomes OnLine Database (GOLD) http://www.genomesonline.org/index.htm Global comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes & metadata http://www.hsls.pitt.edu/molbio

16 Genome Resources http://www.hsls.pitt.edu/molbio

17 Search for organism’s whole genome sequence http://www.hsls.pitt.edu/molbio

18 Genome Resources NCBI:  Genomes Resources : LinkLink Genome: http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome JGI: Integrated Microbial genome LinkLink http://www.hsls.pitt.edu/molbio

19 NCBI Genome http://www.hsls.pitt.edu/molbio

20 NCBI BioProject  Query: Check the status of genome sequencing for an organism, such as honey bee. Answer:  Enter search term under BioProject  Select the appropriate organism  The BioProject summary page will provide information of available projects and sequencing status  Click on Project Type for more detailed information  Explore Related Resources http://www.hsls.pitt.edu/molbio

21 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/rabbit.swf Resources NCBI Genome Project: http://www.ncbi.nlm.nih.gov/genomeprj http://www.ncbi.nlm.nih.gov/genomeprj NCBI Genome: http://www.ncbi.nlm.nih.gov/sites/genome http://www.ncbi.nlm.nih.gov/sites/genome Find the genomic sequence for an organism, such as rabbit.

22 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. CLICK Rabbit http://www.ncbi.nlm.nih.gov/genomeprj http://www.hsls.pitt.edu/molbio

23 NCBI Genome Project : Rabbit Genome http://www.hsls.pitt.edu/molbio

24 NCBI Genome Project : Rabbit Genome http://www.hsls.pitt.edu/molbio

25 Link to the video tutorial: http://media.hsls.pitt.edu/media/molbiovideos/img.swf Resources Integrated Microbial Genome (IMG): http://img.jgi.doe.gov/cgi-bin/w/main.cgi http://img.jgi.doe.gov/cgi-bin/w/main.cgi Find the genomic sequence for a bacteria, such as Salmonella enterica

26 Human genome sequence http://www.hsls.pitt.edu/molbio

27 Genomic achievements since the Human Genome Project http://www.hsls.pitt.edu/molbio

28 http://goo.gl/bsZdN http://www.hsls.pitt.edu/molbio

29 Genome Biology: Structural Variations http://www.hsls.pitt.edu/molbio

30 Genome Reference Consortium Link to the PLoS Biology paper on the GRC : http://goo.gl/30Xunhttp://goo.gl/30Xun http://www.hsls.pitt.edu/molbio

31 NCBI Genome Resources http://www.ncbi.nlm.nih.gov/guide/genomes / http://www.hsls.pitt.edu/molbio

32 What is a Genome Browser? Genome Browsers enable researchers to visualize & browse entire genomes with annotated data including: gene prediction and structure proteins expression regulation variation comparative analysis etc. Annotated data is usually from multiple diverse sources. http://www.hsls.pitt.edu/molbio

33 Eukaryotic Genome Browsers http://www.hsls.pitt.edu/molbio Display: Vertical Display: Horizontal

34 Non-vertebrate Genome Browsers http://www.hsls.pitt.edu/molbio

35 Genome Browsers The Big Three  NCBI MapViewer  UCSC Genome Browser  EBI Ensemble Generic Genome Browser (Gbrowse) Display: Vertical Display: Horizontal http://www.hsls.pitt.edu/molbio

36 UCSC Genome Browser http://www.hsls.pitt.edu/molbio

37 UCSC Genome Browser Default Tracks http://www.hsls.pitt.edu/molbio

38 UCSC Genome Browser Page http://www.hsls.pitt.edu/molbio mRNA and EST Tracks Expression (such as microarray) Comparative Genomics As a group Individual species Variation and Repeats (including SNPs, copy number variation) Groups of data (Tracks) ENCODE Tracks Phenotype and Disease Tracks Regulation (including TFBS)

39 Navigating the Human Genome Browse the region of human chromosome 7 between 54,318043 to 55,974,438 bp (chr7:54,318,043-55,974,438) http://www.hsls.pitt.edu/molbio

40 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/ucsc_genes.swf Resource UCSC Genome Browser: http://genome.ucsc.edu/http://genome.ucsc.edu/ Browse the region of human chromosome 7 between 54,318043 to 55,974,438 bp. What genes are present in this region ?

41 UCSC Genome Browser http://www.hsls.pitt.edu/molbio

42 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

43 UCSC Genome Browser: Navigating a Genomic Region What genes are present in this region? http://www.hsls.pitt.edu/molbio

44 Bioinformatics Institutions http://www.ebi.ac.uk/ http://www.ncbi.nlm.nih.gov/ http://www.hsls.pitt.edu/molbio

45 UCSC Genome Browser: Navigating a Genomic Region What is RefSeq ? http://www.hsls.pitt.edu/molbio

46 NCBI Sequence Databases GenBank  archival database of nucleotide sequences from >160,000 organisms More infoMore info RefSeq  based on GenBank record, non-redundant expert verified databases of reference sequences More infoMore info http://www.hsls.pitt.edu/molbio

47 International Nucleotide Sequence Database Collaboration http://www.hsls.pitt.edu/molbio

48 Primary Vs Derivative databases http://www.hsls.pitt.edu/molbio

49 RefSeq Scope & Accessions Genomic DNA NC_123456 - complete genome, complete chromosome, complete 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/molbio

50 RefSeq Status Codes Provisional Reviewed Predicted Genome Annotation  more about RefSeq status codes more about RefSeq status codes http://www.hsls.pitt.edu/molbio

51 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

52 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

53 Display Options http://www.hsls.pitt.edu/molbio  Hide: removes a track from view  Dense: all items collapsed into a single line  Squish: each item = separate line, but 50% height + packed  Pack: each item separate, but efficiently stacked (full height)  Full: each item on separate line

54 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

55 Gene Description http://www.hsls.pitt.edu/molbio

56 Gene Description http://www.hsls.pitt.edu/molbio Informative description other resource links microarray data mRNA secondary structure links to sequences protein domains/structure orthologs in other species Gene Ontology™ descriptions mRNA descriptions pathways genetic association studies comparative toxicology gene model

57 UCSC Genome Browser: Navigating a Genomic Region Find SNPs present in this region http://www.hsls.pitt.edu/molbio

58 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/ucsc_snp.swf File: UCSC_part2.swf Resource UCSC Genome Browser: http://genome.ucsc.edu/http://genome.ucsc.edu/ Browse the region of human chromosome 7 between 55,033,691 to 55,282,150 bp. What genetic variations are present in this region ? Retrieve the DNA sequence of this genomic region showing SNPs in red and all gene exons in blue

59 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

60 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

61 UCSC Genome Browser: Navigating a Genomic Region http://www.hsls.pitt.edu/molbio

62 BLAT: Map a protein sequence into the genome http://www.hsls.pitt.edu/molbio

63 UCSC Blat: Place a Peptide Seq into the Genome Peptide Seq: NKSSHFYSNVGLQIQTYELQESNVQLKLTVVET Nucleotide seq: AAATCCTCACATTTTTACTCAA ATGTTGGACTTCAAATTCAGACAT ATGAACTTCAGGAAAGC AATGTTCA http://www.hsls.pitt.edu/molbio

64 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/blat.swf File: Blat.swf Resource UCSC BLAT: http://genome.ucsc.edu/cgi-bin/hgBlat?command=starthttp://genome.ucsc.edu/cgi-bin/hgBlat?command=start Place a mRNA or peptide sequence into the human genome

65 UCSC Blat http://genome.ucsc.edu/cgi-bin/hgBlat http://www.hsls.pitt.edu/molbio

66 UCSC Blat http://www.hsls.pitt.edu/molbio

67 UCSC Blat Peptide Seq: NKSSHFYSNVGLQIQTYELQESNVQLKLTVVET http://www.hsls.pitt.edu/molbio

68 Thank you! Any questions? Carrie IwemaAnsuman Chattopadhyay iwema@pitt.eduansuman@pitt.edu 412-383-6887412-648-1297 http://www.hsls.pitt.edu/molbio

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