genomes at ncbi. database and tool explosion 3 2000 : 230 databases and tools 1996 : first annual...
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Database and Tool Explosion : 230 databases and tools 1996 : first annual compilation of databases and tools lists 57 databases and tools The annual database issue of NAR (Nucleic Acids Research) has grown exponentially 2009: 1170 databases and toolsTRANSCRIPT
Genomes at NCBI Genomes at NCBI
Genomes at NCBI Genomes at NCBI
Database and Tool ExplosionDatabase and Tool Explosion
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2000: 230 databases and tools
1996: first annual compilation of databases and tools lists 57 databases and tools
The annual databaseissue of NAR (Nucleic AcidsResearch) has grownexponentially
2009: 1170 databases and tools
NCBIMap ViewerEBI
Ensembl
Genome BrowsersGenome Browsers
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UCSCGenome Browser
Organizing the GenomeOrganizing the Genome
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genes & predictions
variations and mutations
cross-speciescomparative data
and many more types of data from expressionand regulation to mRNA and ESTs…
Gene X
DescriptionTranscript dataStructureGene OntologyPathway DataHomologous GenesExpression DataEtc….
UCSC Genome Browser: genome.ucsc.eduUCSC Genome Browser: genome.ucsc.edu
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UCSC Genome UCSC Genome BrowserBrowser
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A sample of what we can find:A sample of what we can find: 8
gene details
comparisons
SNPs
Ann
otat
ion
Trac
ks
officialsequence
The Genome Browser GatewayThe Genome Browser Gatewaystart page, basic searchstart page, basic search
Use this Gateway to search by:◦ Gene names, symbols◦ Chromosome number: chr7, or region: chr11:1038475-1075482◦ Keywords: kinase, receptor◦ IDs: NP, NM, OMIM, and more…
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text/ID searches
The Genome Browser GatewayThe Genome Browser Gatewaystart page choices, December 2006start page choices, December 2006
Make your Gateway choices:1. Select Clade2. Select species: search 1 species at a time3. Assembly: the official backbone DNA sequence4. Position: location in the genome to examine
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1 42 3
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The Genome Browser GatewayThe Genome Browser Gatewaysample search for Human TP53sample search for Human TP53
Sample search: human, March 2006 assembly, tp53
select
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Overview of the wholeOverview of the wholeGenome Browser pageGenome Browser page
}Genome viewer section
mRNA and EST Tracks
Expression and Regulation
Comparative Genomics
Variation and Repeats
Groups of data
Mapping and Sequencing Tracks
Genes and Gene Prediction Tracks
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Sample Genome Viewer image, Sample Genome Viewer image, TP53 regionTP53 region
base positionSTS markers
Known genes
17 species compared
single species compared
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Options for Changing Images: Options for Changing Images: Upper SectionUpper Section
Change your view or location with controls at the top
Use “base” to get right down to the nucleotidesConfigure: to change font, window size, more…
Specifya
position
Walkleft orright
Zoomin
Zoomout
click tozoom 3x
and re-center
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Annotation Track display optionsAnnotation Track display options
Some data is ON or OFF by default
Links to infoand/or filters
Menu links to info about the tracks: content, methods You change the view with pulldown menus
enforcechanges
After making changes, REFRESH to enforce the change
Change track view
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Annotation Track options, definedAnnotation Track options, definedHide: 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
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Reset, Hide, Configure or Refresh to change Reset, Hide, Configure or Refresh to change settingssettings
reset, back to defaults start from
scratch
enforce any changes (hide, full, squish…)
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Click Any Viewer Object for DetailsClick Any Viewer Object for Details
Example: click your mouse anywhere on the TP53 line
Click the item
New web page
opens
Many details and links to more data about TP53
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Click annotation track item Click annotation track item for details pages for details pages
Not all genes have this much detail.
informativedescriptionother resource links
microarray data
mRNA secondary structure
links to sequences
protein domains/structure
homologs in other species
Gene Ontology™ descriptions
mRNA descriptions
pathways
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Get DNA, with Extended Case/Color OptionsGet DNA, with Extended Case/Color Options
Use the DNA link at the top
Plain or Extended options
Change colors, fonts, etc.
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Get Sequence from Details PagesGet Sequence from Details PagesClick a track, go to Sequence section of details page
Click the line Click the item
sequence sectionon detail page
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Accessing the BLAT toolAccessing the BLAT tool
BLAT = BLAST-like Alignment Tool
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BLAT tool overview: BLAT tool overview:
Make choices
Paste one or more
sequences
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BLAT results, with linksBLAT results, with links
go to
bro
wse
r/vie
wer
go to
alig
nmen
t det
ail
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BLAT results, BLAT results, browser linkbrowser link
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BLAT results,BLAT results,alignment alignment detailsdetails
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Proteome BrowserProteome Browser
Access from homepage or Known Gene pages
Exon diagram, amino acids…
Many protein properties (pI, mw, composition, 3D…)
more data
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In-Silico PCR: In-Silico PCR: Find Find genomicgenomic sequence using primers sequence using primers