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Genomes at NCBI

Genomes at NCBI. Genomes at NCBI. Database and Tool Explosion. 2000 : 230 databases and tools. 1996 : first annual compilation of databases and tools lists 57 databases and tools. 2009: 1170 databases and tools. The annual database issue of NAR (Nucleic Acids Research) has grown

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Genomes at NCBI

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  1. Genomes at NCBI

  2. Genomes at NCBI

  3. Database and Tool Explosion 2000: 230 databases and tools 1996: first annual compilation of databases and tools lists 57 databases and tools 2009: 1170 databases and tools The annual database issue of NAR (Nucleic Acids Research) has grown exponentially

  4. Genome Browsers UCSC Genome Browser EBI Ensembl NCBI Map Viewer

  5. Organizing the Genome genes & predictions variations and mutations cross-species comparative data Gene X Description Transcript data Structure Gene Ontology Pathway Data Homologous Genes Expression Data Etc…. and many more types of data from expression and regulation to mRNA and ESTs…

  6. UCSC Genome Browser: genome.ucsc.edu

  7. UCSC Genome Browser

  8. gene details comparisons Annotation Tracks SNPs A sample of what we can find: official sequence

  9. text/ID searches The Genome Browser Gatewaystart 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…

  10. 3 2 1 The Genome Browser Gatewaystart page choices, December 2006 4 Make your Gateway choices: • Select Clade • Select species: search 1 species at a time • Assembly: the official backbone DNA sequence • Position: location in the genome to examine

  11. select The Genome Browser Gatewaysample search for Human TP53 • Sample search: human, March 2006 assembly, tp53

  12. Mapping and Sequencing Tracks Genes and Gene Prediction Tracks mRNA and EST Tracks Expression and Regulation Comparative Genomics Variation and Repeats Overview of the wholeGenome Browser page } Genome viewer section Groups of data

  13. STS markers Known genes 17 species compared single species compared Sample Genome Viewer image, TP53 region base position

  14. Options for Changing Images: Upper Section Walk left or right Zoom in Zoom out • Change your view or location with controls at the top • Use “base” to get right down to the nucleotides • Configure: to change font, window size, more… Specify a position click to zoom 3x and re-center

  15. Change track view Annotation Track display options • Some data is ON or OFF by default enforce changes Links to info and/or filters • Menu links to info about the tracks: content, methods • You change the view with pulldown menus • After making changes, REFRESH to enforce the change

  16. 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 Annotation Track options, defined • Hide: removes a track from view

  17. enforce any changes (hide, full, squish…) reset, back to defaults start from scratch Reset, Hide, Configure or Refresh to change settings

  18. Click the item New web page opens Many details and links to more data about TP53 Click Any Viewer Object for Details Example: click your mouse anywhere on the TP53 line

  19. informative description other resource links links to sequences microarray data mRNA secondary structure protein domains/structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways Click annotation track item for details pages Not all genes have this much detail.

  20. Get DNA, with Extended Case/Color Options • Use the DNA link at the top • Plain or Extended options • Change colors, fonts, etc.

  21. Click the line Click the item sequence section on detail page Get Sequence from Details Pages Click a track, go to Sequence section of details page

  22. Accessing the BLAT tool BLAT = BLAST-like Alignment Tool

  23. Make choices • Paste one or more sequences BLAT tool overview:

  24. BLAT results, with links go to browser/viewer go to alignment detail

  25. BLAT results, browser link

  26. BLAT results,alignment details

  27. Proteome Browser • Access from homepage or Known Gene pages • Exon diagram, amino acids… • Many protein properties (pI, mw, composition, 3D…) more data

  28. In-Silico PCR: Find genomic sequence using primers

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