Professional Development Course 1 – - PowerPoint Presentation

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Professional Development Course 1 – - PPT Presentation

Molecular Medicine Genome Biology June 12 2012 Ansuman Chattopadhyay PhD Head Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansumanpittedu ID: 571888

www http genome pitt http www pitt genome hsls molbio ucsc browser region genomic ncbi human navigating media sequence

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Slide1

Professional Development Course 1 –Molecular MedicineGenome BiologyJune 12, 2012

Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.eduhttp://www.hsls.pitt.edu/guides/genetics Slide2

Genomic achievements since the Human Genome Projecthttp://

www.hsls.pitt.edu/molbio Slide3

ObjectiveOrganism Whole Genome Sequence DatabasesGenome Browsers

http://www.hsls.pitt.edu/molbio Slide4

TopicsGenome Sequencing ProjectsNCBI Genome resourcesIntegrated Microbial GenomeUCSC Genome Bioinformatics

Genome BrowsersUCSC Genome BrowserUCSC Table BrowserNCBI Map viewerGeneric Genome Browser (Gbrowse)

http://

www.hsls.pitt.edu/molbio

Slide5

Genome BiologyHuman Genome Project Video

http://www.hsls.pitt.edu/molbio Slide6

Chromosome Structurehttp://

www.hsls.pitt.edu/molbio Slide7

Genome Biology: KaryotypeAdapted from NGHRITrisomy 21

Monosomy X

http://

www.hsls.pitt.edu/molbio Slide8

Genome Biology: KaryotypeNHGRIhttp://www.hsls.pitt.edu/molbio

Slide9

Genome Biology: Molecular Cloning p53

CFTR

NFkB

8 September, 1989

http://

www.hsls.pitt.edu/molbio

Slide10

Genome Biology : Time Line1976

RNA Bacteriophage MS22001Human Genome

Draft Seq

2003

Published Complete

Human Ref Genome

2007

Diploid Genome

seq

an Individual Human

2011

Published Complete

Genomes: 1863 organisms

1995

Haemophilus

Influenza

2008

Jim Watson

Genome

Yeast

1996

1998

elegans

2002

Drosophila

http://www.hsls.pitt.edu/molbioSlide11

DNA Sequencing Cost

http://www.hsls.pitt.edu/molbio Slide12

Oxford NanoporeA 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 Slide13

Organism Whole Genome Sequences2001

2012

http://

www.hsls.pitt.edu/molbio

Slide14

Organism Whole Genome Sequences

Human

Mouse

Rat

Dog

Cow

Chimp

Rabbit

……..

http://

www.hsls.pitt.edu/molbio

Slide15

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/molbioSlide16

Genome Resourceshttp://www.hsls.pitt.edu/molbioSlide17

Search for organism’s whole genome sequencehttp://www.hsls.pitt.edu/molbio Slide18

Genome ResourcesNCBI:Genomes Resources : LinkGenome: http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeJGI: Integrated Microbial genome Link

http://www.hsls.pitt.edu/molbio Slide19

NCBI Genomehttp://www.hsls.pitt.edu/molbioSlide20

NCBI BioProjectQuery: Check the status of genome sequencing for an organism, such as honey bee.Answer:Enter search term under

BioProjectSelect the appropriate organismThe 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/molbioSlide21

http://www.hsls.pitt.edu/molbio

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/rabbit.swf ResourcesNCBI Genome Project: http://www.ncbi.nlm.nih.gov/genomeprjNCBI Genome: http://www.ncbi.nlm.nih.gov/sites/genome

Find the genomic sequence for an organism, such as

rabbit.Slide22

NCBI Genome ProjectA 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.

CLICKRabbithttp://www.ncbi.nlm.nih.gov/genomeprj

http://

www.hsls.pitt.edu/molbio

Slide23

NCBI Genome Project : Rabbit Genome

http://www.hsls.pitt.edu/molbio Slide24

NCBI Genome Project : Rabbit Genome

http://www.hsls.pitt.edu/molbio Slide25

http://www.hsls.pitt.edu/molbio

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

Salmonella entericaSlide26

Human genome sequencehttp://www.hsls.pitt.edu/molbio Slide27

Genomic achievements since the Human Genome Project

http://www.hsls.pitt.edu/molbio Slide28

http://goo.gl/bsZdN

http://www.hsls.pitt.edu/molbio Slide29

Genome Biology: Structural Variations

http://www.hsls.pitt.edu/molbio Slide30

Genome Reference Consortium Link to the PLoS Biology paper on the GRC : http://goo.gl/30Xun

http://www.hsls.pitt.edu/molbio Slide31

NCBI Genome Resourceshttp://www.ncbi.nlm.nih.gov/guide/genomes/

http://www.hsls.pitt.edu/molbio Slide32

What is a Genome Browser?Genome Browsers enable researchers to visualize & browse entire genomes with annotated data including:gene prediction and structure proteins

expressionregulationvariationcomparative analysisetc. Annotated data is usually from multiple diverse sources.

http://

www.hsls.pitt.edu/molbio

Slide33

Eukaryotic Genome Browsershttp://www.hsls.pitt.edu/molbio

Display: Vertical

Display: HorizontalSlide34

Non-vertebrate Genome Browsershttp://www.hsls.pitt.edu/molbioSlide35

Genome BrowsersThe Big ThreeNCBI MapViewerUCSC Genome BrowserEBI EnsembleGeneric Genome Browser (Gbrowse

)

Display: Vertical

Display: Horizontal

http://

www.hsls.pitt.edu/molbio

Slide36

UCSC Genome Browserhttp://www.hsls.pitt.edu/molbio Slide37

UCSC Genome Browser Default Trackshttp://www.hsls.pitt.edu/molbioSlide38

UCSC Genome Browser Pagehttp://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)

Slide39

Navigating the Human GenomeBrowse 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 Slide40

http://www.hsls.pitt.edu/molbio

Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/ucsc_genes.swf ResourceUCSC Genome Browser: 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 ?

Slide41

UCSC Genome Browser

http://www.hsls.pitt.edu/molbio Slide42

UCSC Genome Browser: Navigating a Genomic Region

http://www.hsls.pitt.edu/molbioSlide43

UCSC Genome Browser: Navigating a Genomic Region

What genes are present in this region?http://www.hsls.pitt.edu/molbioSlide44

Bioinformatics Institutionshttp://www.ebi.ac.uk/http://www.ncbi.nlm.nih.gov/

http://www.hsls.pitt.edu/molbio

Slide45

UCSC Genome Browser: Navigating a Genomic RegionWhat is

RefSeq ?http://www.hsls.pitt.edu/molbioSlide46

NCBI Sequence DatabasesGenBankarchival database of nucleotide sequences from >160,000 organisms More info RefSeqbased on GenBank record, non-redundant expert verified databases of reference sequences

More info http://www.hsls.pitt.edu/molbioSlide47

International Nucleotide Sequence Database Collaborationhttp://www.hsls.pitt.edu/molbioSlide48

Primary Vs Derivative databaseshttp://www.hsls.pitt.edu/molbioSlide49

RefSeq Scope & AccessionsGenomic 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/molbioSlide50

RefSeq Status CodesProvisional Reviewed Predicted Genome Annotation more about RefSeq status codes

http://www.hsls.pitt.edu/molbioSlide51

UCSC Genome Browser: Navigating a Genomic Region

http://www.hsls.pitt.edu/molbioSlide52

UCSC Genome Browser: Navigating a Genomic Region

http://www.hsls.pitt.edu/molbioSlide53

Display Optionshttp://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)