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BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
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BITS: UCSC genome browser - Part 1

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These are the first lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser. …

These are the first lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser.

See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203990:orange-genome-browsers-ucsc-training&catid=81:training-pages&Itemid=190

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Transcript

  • 1. UCSCgenome browsing Paco Hulpiau http://www.bits.vib.be
  • 2. Introduction§ Browse genes in their genomic context§ See features in and around a specific gene§ Investigate genome organization and explore larger chromosome regions§ Search and retrieve information on a gene- and genome-scale§ Compare genomes
  • 3. Introduction§ Collaboration between main genome browsers Ensembl, UCSC and NCBI » use same genome assemblies » interlinking between sites§ Ensembl Genome Browser: http://www.ensembl.org/§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/§ UCSC Genome Browser: http://genome.ucsc.edu/
  • 4. Introduction
  • 5. Introduction
  • 6. Introduction
  • 7. Introduction
  • 8. Introduction
  • 9. Introduction§ Collaboration between main genome browsers Ensembl, UCSC and NCBI » use same genome assemblies » interlinking between sites§ Ensembl Genome Browser: http://www.ensembl.org/§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/§ UCSC Genome Browser: http://genome.ucsc.edu/
  • 10. Introduction
  • 11. Introduction
  • 12. Introduction§ Collaboration between main genome browsers Ensembl, UCSC and NCBI » use same genome assemblies » interlinking between sites§ Ensembl Genome Browser: http://www.ensembl.org/§ NCBI Map Viewer: http://www.ncbi.nlm.nih.gov/mapview/§ UCSC Genome Browser: http://genome.ucsc.edu/
  • 13. Introduction
  • 14. Introduction
  • 15. Introduction
  • 16. Introduction§ Other genome browsers and genome databases:http://genome.jgi-psf.org Eukaryotic (143) and prokaryotic (505) genomeshttp://www.xenbase.org Xenopus tropicalishttp://flybase.org Drosophila genes & genomeshttp://www.wormbase.org C. elegans and some related nematodeshttp://www.tigr.org => http://www.jcvi.org/ Comprehensive Microbial Resource (CMR) => http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgihttp://genolist.pasteur.fr Microbial genomes
  • 17. Introduction
  • 18. Introduction
  • 19. § The UCSC Genome browser was created by the Genome Bioinformatics Group at the University of California Santa Cruz (UCSC). http://genome.ucsc.edu/
  • 20. § The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide.
  • 21. § Blat quickly maps your sequence to the genome. BLAT is not BLAST !BLAT works by keeping an index of the entire genome in memory.The index consists of all non-overlapping DNA 11-mers or protein 4-mers.The index is used to find areas of probable homology, which are thenloaded into memory for a detailed alignment.BLAT on DNA can quickly find sequences of 95% and greater similarityof length 40 bases or more.BLAT on proteins finds sequences of 80% and greater similarity of length20 amino acids or more.
  • 22. § The Table Browser provides convenient access to the underlying database.
  • 23. § The Gene Sorter displays a sorted table of genes that are related to one another. The relationship can be one of several types, including protein-level homology, similarity of gene expression profiles, or genomic proximity.
  • 24. § In-Silico PCR searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance.§ When successful, the search returns a file (fasta) containing all sequences in the database that lie between and include the primer pair.
  • 25. § Genome Graphs is a tool for displaying genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping.
  • 26. § Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything.§ You can analyze multiple alignments, compare genomic annotations and much more...
  • 27. § VisiGene lets you browse through a large collection of in situ mouse and frog images.
  • 28. § The Proteome Browser provides a wealth of protein information presented in the form ofgraphical images of tracks and histograms and links to other sites.
  • 29. § The Utilities page contains links to some tools created by the UCSC Genome Bioinformatics Group.§ DNA Duster & Protein Duster remove non-sequence related characters from an input sequence.
  • 30. § The Utilities page contains links to some tools created by the UCSC Genome Bioinformatics Group.§ DNA Duster & Protein Duster remove non-sequence related characters from an input sequence.
  • 31. Clade – Genome - Assembly
  • 32. GENOMEBROWSERDISPLAY
  • 33. POSITIONCONTROL
  • 34. TRACKCONTROL
  • 35. Navigation: position control
  • 36. Navigation: position control§ Click the zoom in and zoom out buttons on top to zoom in or out 1.5, 3 or 10-fold on the center of the window
  • 37. Navigation: position control§ Zoom in 3-fold by clicking anywhere on the base position track§ Zoom to a specific region using “drag and zoom”
  • 38. Navigation: position control§ To scroll the view of the display horizontally by set increments of 10%, 50% or 95% of the displayed size (as given in base pairs) click the corresponding move arrow
  • 39. Navigation: position control§ To scroll the left of right side by a specified number of vertical gridlines while keeping the opposite side fixed click the appropriate move start or move end arrow
  • 40. Navigation: position control§ To display a (completely) different position enter the new location in the position/search text box§ You can also jump to an other gene location
  • 41. Annotation Tracks TRACKCONTROL
  • 42. HIDE = removes a track from viewFULL = each item on a separate line
  • 43. DENSE = all items collapsed into single line SQUISH = all items on several lines PACKED and at 50% height PACK = each item separate and efficiently stacked (full height)
  • 44. Annotation Tracks
  • 45. Annotation Tracks§ Different genome/assembly => different tracks!
  • 46. Annotation Tracks
  • 47. Annotation Tracks
  • 48. Annotation Tracks
  • 49. Annotation Tracks
  • 50. Annotation Tracks
  • 51. Annotation Tracks
  • 52. Annotation Tracks
  • 53. Annotation Tracks§ Now try to change the tracks as follows
  • 54. Annotation Tracks§ and...
  • 55. DENSE FULLSQUISHSQUISHPACK
  • 56. direction of transcriptionUTR EXON EXON INTRON
  • 57. Annotation Tracks
  • 58. Annotation Tracks
  • 59. Annotation Tracks
  • 60. Annotation Tracks
  • 61. Annotation Tracks
  • 62. Annotation Tracks
  • 63. Annotation Tracks
  • 64. Annotation Tracks
  • 65. Browser graphics in PDF TABLE GET CURRENT BROWSER DNA BROWSER GRAPHIC IN PDF TO GET OTHERCLICK DATALINE
  • 66. 1 CURRENT BROWSER GRAPHIC IN PDFTO GETOTHER DATA
  • 67. Exercises (I)1) Search for your gene of interest on Human Feb. 2009 (GRCh37/hg19) Assembly » Include 1000 base pairs up- and downstream » Only show the tracks: RefSeq Genes (pack) Conservation (full, primates only) » Save graphical view as PDF (exercises1_1)
  • 68. Exercises (I)2) How many transcripts are there? » Compare UCSC Genes with RefSeq and Ensembl genes! » Save graphical view as PDF (exercises1_2)
  • 69. Exercises (I)3) What are the flanking genes? Are these conserved outside mammals? » Zoom out until you can see at least two or three flanking genes (may need to hide some tracks, leave RefSeq on) » Now have a look in the chicken genome » Save graphical view as PDF (exercises1_3a en exercises1_3b)
  • 70. Exercises (I)4) Is there any regulatory information available? » Change the view to see the genomic region upstream (exon 1 and ~2000 upstream) and open some regulatory tracks e.g. ORegAnno, TFBS Conserved, TS miRNA sites » Save graphical view as PDF (exercises1_4)

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