1 / 68

Professional Development Course 1 – Molecular Medicine Genome Biology June 12 , 2012

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.

marlie
Download Presentation

Professional Development Course 1 – Molecular Medicine Genome Biology June 12 , 2012

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Professional Development Course 1 –Molecular MedicineGenome BiologyJune 12, 2012 AnsumanChattopadhyay, 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 Trisomy 21 Monosomy X Adapted from NGHRI http://www.hsls.pitt.edu/molbio

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

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

  10. Genome Biology : Time Line RNA Bacteriophage MS2 Human Genome Draft Seq Diploid Genome seq of an Individual Human Yeast Drosophila 1976 2002 2001 2007 1996 2011 1995 1998 2003 2008 Haemophilus Influenza C. elegans Published Complete Human Ref Genome Published Complete Genomes: 1863 organisms Jim Watson Genome 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 2001 2012 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 : Link • Genome: http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome • JGI: Integrated Microbial genome Link 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.  Find the genomic sequence for an organism, such as rabbit. • Resources • NCBI Genome Project: http://www.ncbi.nlm.nih.gov/genomeprj • NCBI Genome: http://www.ncbi.nlm.nih.gov/sites/genome Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/rabbit.swf http://www.hsls.pitt.edu/molbio

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

  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/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 Display: Vertical Display: Horizontal http://www.hsls.pitt.edu/molbio

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

  35. Genome Browsers Display: Vertical • The Big Three • NCBI MapViewer • UCSC Genome Browser • EBI Ensemble • Generic Genome Browser (Gbrowse) 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. Phenotype and Disease Tracks mRNA and EST Tracks Regulation (including TFBS) Expression (such as microarray) • Comparative Genomics • As a group • Individual species Variation and Repeats (including SNPs, copy number variation) ENCODE Tracks UCSC Genome Browser Page Groups of data (Tracks) http://www.hsls.pitt.edu/molbio

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

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

  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 organismsMore info • RefSeq • based on GenBank record, non-redundant expert verified databases of reference sequences More 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 http://www.hsls.pitt.edu/molbio

More Related