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Tools in Bioinformatics

Tools in Bioinformatics. Genome Browsers. Retrieving genomic information. Previous lesson(s): annotation-based perspective of search/data Today: genomic-based perspective: look at all the data from the prism of a specific chromosome location Next: sequence-based searches. Genome browsers.

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Tools in Bioinformatics

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  1. Tools in Bioinformatics Genome Browsers

  2. Retrieving genomic information • Previous lesson(s): annotation-based perspective of search/data • Today: genomic-based perspective: look at all the data from the prism of a specific chromosome location • Next: sequence-based searches

  3. Genome browsers • NCBI Map Viewer • http://www.ncbi.nih.gov/mapview • Ensembl • http://www.ensembl.org/ • UCSC Genome Browser • http://genome.ucsc.edu/

  4. navigate navigate UCSC Home page ( genome.ucsc.edu ) General information Specific information— new features, current status, etc. UCSC Material developed by W.C. Lathe and M. Mangan, info@openhelix.com

  5. Start all text/ID searches here! Helpful search examples, suggestions below The Genome Browser Gatewaystart page, basic search Use this Gateway page to search by: gene names, gene symbols, chromosome number, region, keyword, identifiers (NP, NM, OMIM, LocusLink), and more. See examples on page for format

  6. Use the Submit button to send the query to the database. The Genome Browser Gatewaystart page choices, sample search for Human BRCA1 Perform a sample search with the May 2004 data assembly, and examine the results. We will use human BRCA1 as our example. breast and ovarian cancer susceptibility gene, Science. 1994 Oct 7;266(5182):66-71

  7. select Results of our sample search • Often you will have to select the right gene from a results list • Sometimes, you will go directly to a browser image (use an ID)

  8. Overview of the wholeGenome Browser page(first day, new human release) } Genome viewer section Track and image controls (day 1 = 40 tracks)

  9. Track and image controls (72 tracks = mature assembly) Groups of data Mapping and Sequencing Tracks Genes and Gene Prediction Tracks mRNA and EST Tracks Expression and Regulation Comparative Genomics ENCODE Tracks Variation and Repeats Overview of the wholeGenome Browser page(mature release) } Genome viewer section

  10. Genome backbone STS markers Known genes RefSeq genes Gene predictions Full-length clones if available GB human ESTs, mRNAs Microarray data if available species comparisons repeats First sample Genome Viewer image

  11. Different species, different tracks

  12. Tick marks; a single location (STS, SNP) exon < < < exon < exon < < < < ex 3' UTR 5' UTR Intron, and direction of transcription <<< or >>> Track colors may have meaning—for example, Known Gene track: • If there is a corresponding PDB entry, = black • If there is a corresponding NCBI Reviewed seq, = dark blue • If there is a corresponding NCBI Provisional seq, = light blue For some tracks, the height of a bar is increased likelihood of an evolutionary relationship Visual Cues on the Genome Browser

  13. Walk left or right Zoom in Zoom out Specify a position How wide on screen Options for changing the images: • Change your overview from the controls at the top • Change viewer window size • Use “base” to get right down to the nucleotides

  14. Click on a line in the annotation tracks for more info… First sample Genome Viewer image

  15. Click the line New web page opens Many links to more data about BRCA1 Clicking an annotation line, new page of detailed information You will get detail for that single item Example: click on the BRCA1 Black Known Genes line

  16. “Known gene” BRCA1 sample page informative description other resource links links to sequences microarray data Not all genes have this much detail. Different annotation tracks carry different detail data. mRNA secondary structure protein domains and structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways

  17. Extended options to set colors, case, underline Getting the sequences2 ways: get DNA or Extended options Use the DNA link at the top of the Viewer, simple or extended options Choices here reflect displayed tracks

  18. Click the line From the gene detail new page go to Sequence section: Simple sequences, just this known gene Getting the sequencesFrom Gene Detail page Click a track, link down two levels to get that specific sequence

  19. refresh to make changes Change track view Links to details and/or filters Menu links to info about tracks—content and methods. You change the view with pulldown menus. After changing a pulldown, REFRESH to commit the change Annotation Track display optionshide, dense, squish, pack, full…? Some data is ON or OFF by default

  20. Hide: removes a track from your image. • Dense: all items collapsed into a single line. • Squish: each item = separate line, but 50% height + packed • Pack: each item separate, but efficiently stacked (but full height) • Full: each item on a separate line. Annotation Track options, defined

  21. OR To clear your “cart” or parameters, click reset all Annotation Track options, if altered….important point: the browser remembers! • Session information (the position you were examining) • Track choices (squish, pack, full, etc) • Filter parameters (if you changed the colors of any items, or the subset to be displayed) …are all saved on your computer. When you come back in a couple of days to use it again, these will still be set. You may—or may not—intend this.

  22. make the changes specified (hide, full, squish, dense…) back to defaults to start from scratch Other image display options new! You control the view, with pulldown menus and these other options.

  23. Table browser: Output formats • Fasta file of sequence data

  24. SFRS5 examples

  25. SFRS11 Example

  26. SFRS7

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