introduction to biocomputing biology in silico 3 rd february 2010

Introduction to BioComputingBiology in silico3rd February 2010

Carrie Iwema, PhD, MLSMolecular Biology Information SpecialistHealth Sciences Library SystemUniversity of [email protected]

http://www.hsls.pitt.edu/guides/genetics

mailto:[email protected]


General Topics

Information Overload

Genome Gene Protein



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

Entrez Gene UniProt



Information Overload

209K• Breast

Cancer

84K• Colon

Cancer

52K • p53

4K • STAT1

5,394 Journals


1.3 billionsearches in 2009


Alternatives to PubMed



http://pubget.com/search

http://www.gopubmed.org/web/gopubmed/

http://www.novoseek.com/Welcome.action

http://www.ncbi.nlm.nih.gov/pubmed

Growth of Molecular Databases

Source: Nodal Point Blog

2008: 1075


2009: 1170

2010: 1230


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://nar.oxfordjournals.org/content/vol38/suppl_1/index.dtl




http://bioinformatics.oxfordjournals.org/

http://www.biomedcentral.com/bmcbioinformatics/

http://www.biomedcentral.com/bmcbioinformatics/

http://database.oxfordjournals.org/

http://www.ncbi.nlm.nih.gov/pubmed

http://www.ncbi.nlm.nih.gov/mesh


HSLS Molecular Biology Information Service

Workshops

Website

Software Licensing

Bioinformatics Consultations




HSLS OBRC



HSLS OBRC in Science

HSLS OBRC

2441 links to databases

and software

~3000hits/day



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/search_molbio_help


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



Genome Biology



From Cell to Gene

Human Genome Project Video



http://www.youtube.com/watch?v=_EK3g6px7Ik

Genome Biology Time Line

1976

RNA Bacteriophage MS2

2001

Human Genome Draft Seq

2003

Published Complete Human Ref Genome

2007

Diploid Genome seq ofan Individual Human

2010

Published Complete Genomes: 1191 organisms

1995

HaemophilusInfluenza

Human Genome Project Video

2008

Jim Watson Genome


http://www.genome.gov/25019885


Genome Resources

NCBI: Genomes Resources : Link

Genome Project Genome: 6108 species

Genomes OnLine Database (GOLD): Link

JGI: Integrated Microbial Genomes: Link


http://www.ncbi.nlm.nih.gov/guide/genomes/

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

http://www.ncbi.nlm.nih.gov/sites/genome

http://genomesonline.org/index2.htm

http://img.jgi.doe.gov/cgi-bin/pub/main.cgi


NCBI Genome Resources



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.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj


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.

CLICKRabbit



NCBI Genome Project : Rabbit Genome



NCBI Entrez Genome:



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, 1998http://www.hsls.pitt.edu/guides/genetics

http://genomesonline.org/index2.htm


Genome Browsers



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://en.wikipedia.org/wiki/Genome


Genome Browsers The Big Three

NCBI MapViewer UCSC Genome Browser EBI Ensembl

Generic Genome Browser (Gbrowse) JBrowse (Ajax based like Google Map)

Display: Vertical

Display: Horizontal


http://www.ncbi.nlm.nih.gov/mapview/


http://genome.ucsc.edu/cgi-bin/hgGateway

http://uswest.ensembl.org/index.html

http://uswest.ensembl.org/index.html

http://www.gbrowse.org/wiki/index.php/Main_Page

http://jbrowse.org/

http://jbrowse.org/


Tutorial Articles

Link Link

Link Link


http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WG1-4SN8V4K-1-8&_cdi=6809&_user=10&_orig=search&_coverDate=08/31/2008&_sk=999079997&view=c&wchp=dGLzVlz-zSkzk&md5=5be629f1062668e09216dd73510cd45c&ie=/sdarticle.pdf

http://www.currentprotocols.com/protocol/mb1909

http://www.genetics.ucla.edu/ughg/start.html

http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml


Tutorial/Seminar Videos

Link Link

Link Link


http://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?query=genome+browser&input-form=simple&v:project=Molbio_Videos&submit=Search

http://videocast.nih.gov/ram/ctgas012505.ram

http://hstalks.com/main/browse_talk_info.php?talk_id=1395&c=252

http://www.youtube.com/watch?v=z7pZ6JvD8RI&feature=youtube_gdata


UCSC Genome Browser



http://genome.ucsc.edu/cgi-bin/hgGateway

Navigating the Human Genome

Browse the region of human chromosome 7 between bp 54,318,043 to 55,974,438

UCSC Genome Browser


http://genome.ucsc.edu/


UCSC Genome Browser: navigating a genomic region

Set up basic browser parameters




Start fresh





What genes are present in this region?



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.ncbi.nlm.nih.gov/RefSeq/

http://www.ncbi.nlm.nih.gov/Genbank/


International Nucleotide Sequence Database Collaboration



Primary Vs Derivative databases



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.ncbi.nlm.nih.gov/RefSeq/key.html#accessions







Zoom in and display only the EGFR gene




Select the gene region from the “Scale” track to zoom in





Display all Single Nucleotide polymorphisms (SNPs) present in this gene





Retrieve the nucleotide sequence of this genomic region showing all exons in blue and SNPs in Red,

bold faced and underlined.



UCSC Genome Browser: navigating a genomic region: sequence view





Look in probable promoter region and see if there’s anything

interesting…





Zoom out




What transcription factors bind in this region?



Discovery Tool…



NCBI MapViewer



NCBI MapViewer How To: View/download features around an object or

between two objects on a chromosomeStarting with...CHROMOSOMAL COORDINATES

Begin on the Map Viewer home page. Click the "R" icon under Tools for the desired organism and build.

Select the chromosome, enter the coordinates in the From and To boxes, and click Go. Use either exact coordinates, e.g., 61551076, or values such as, 61M or 61551K.

If necessary, use the Maps & Options dialog box to change displayed maps; the maps and region displayed determine the data available.


http://www.ncbi.nlm.nih.gov/projects/mapview/static/MapViewerHelp.html#DisplaySettings

Entrez Gene



Common Questions

What is its function?

What are its neighboring genes?

What is its genomic seq?How many splice varients are there?

What are its intron-exon architechure?

What diseases are associated with it?

Which tissues it expressed ?

How can I get its cDNA clone?



SNP

Genomic Sequence

Expression Profile

Interacting Partners3D Structure

mRNA Sequence

Chromosomal Localization

Disease

Amino acid Sequence

Homologous Sequences


NCBI : Entrez Gene


Entrez GeneFind: gene symbols and aliases sequences: genomic, mRNA, protein intron-exon architecture genomic context: neighboring and

antisense genes interacting partners associated gene ontology terms:

function, cellular component and biological process



Entrez Gene

a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer

each record represents a single gene from a given organism


http://www.ncbi.nlm.nih.gov/RefSeq/


Entrez Gene Sequences

mRNA Seq

Protein Seq

Genomic Seq



Entrez Gene Links



Gene Ontology (GO)

Controlled vocabulary tagging

Function Biological Processes Cellular Component


http://www.geneontology.org/


Entrez Gene: Gene Table


Introns/Exons


Try it!

Find mRNA sequence for your gene of interest



Find mRNA Sequence for Reelin Gene



FASTA vs GenBank records



NCBI Entrez Gene Tutorials

Information page with wiki, video, blog etc.

Entrez gene: A Directory of Genes, NCBI Handbook

Short Video Tutorial (MIT)


http://www.kosmix.com/topic/entrez_gene?

http://www.kosmix.com/topic/entrez_gene?

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch19



http://www.youtube.com/watch?v=rgjQA57PFkY&feature=youtube_gdata


UCSC Genome Browser: find a gene in the genome



Bioinformatics Databases & Software Providers

NCBI Home page Site map Resource Guide

EBI Home page Databases Software


http://www.ncbi.nlm.nih.gov/

http://www.ncbi.nlm.nih.gov/Sitemap/AlphaList.html

http://www.ncbi.nlm.nih.gov/Sitemap/ResourceGuide.html

http://www.ebi.ac.uk/

http://www.ebi.ac.uk/Databases/

http://www.ebi.ac.uk/Tools/


UniProt



UniProt

world's most comprehensive catalog of information on proteins


a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR


UniProt



UniProt



http://www.uniprot.org/uniprot/P00533

Thank you!Any questions?

Carrie Iwema Ansuman [email protected] [email protected] 412-383-6887 412-648-1297





introduction to biocomputing biology in silico 3 rd february 2010

Documents

human genome project

link http

journals http

ncbi genome resources

science http

pubmed http

genome resourcesncbi

desired genome project