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.

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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BITS: UCSC genome browser - Part 1

  1. 1. UCSCgenome browsing Paco Hulpiau http://www.bits.vib.be
  2. 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. 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. 4. Introduction
  5. 5. Introduction
  6. 6. Introduction
  7. 7. Introduction
  8. 8. Introduction
  9. 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. 10. Introduction
  11. 11. Introduction
  12. 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. 13. Introduction
  14. 14. Introduction
  15. 15. Introduction
  16. 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. 17. Introduction
  18. 18. Introduction
  19. 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. 20. § The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide.
  21. 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. 22. § The Table Browser provides convenient access to the underlying database.
  23. 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. 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. 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. 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. 27. § VisiGene lets you browse through a large collection of in situ mouse and frog images.
  28. 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. 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. 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. 31. Clade – Genome - Assembly
  32. 32. GENOMEBROWSERDISPLAY
  33. 33. POSITIONCONTROL
  34. 34. TRACKCONTROL
  35. 35. Navigation: position control
  36. 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. 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. 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. 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. 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. 41. Annotation Tracks TRACKCONTROL
  42. 42. HIDE = removes a track from viewFULL = each item on a separate line
  43. 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. 44. Annotation Tracks
  45. 45. Annotation Tracks§ Different genome/assembly => different tracks!
  46. 46. Annotation Tracks
  47. 47. Annotation Tracks
  48. 48. Annotation Tracks
  49. 49. Annotation Tracks
  50. 50. Annotation Tracks
  51. 51. Annotation Tracks
  52. 52. Annotation Tracks
  53. 53. Annotation Tracks§ Now try to change the tracks as follows
  54. 54. Annotation Tracks§ and...
  55. 55. DENSE FULLSQUISHSQUISHPACK
  56. 56. direction of transcriptionUTR EXON EXON INTRON
  57. 57. Annotation Tracks
  58. 58. Annotation Tracks
  59. 59. Annotation Tracks
  60. 60. Annotation Tracks
  61. 61. Annotation Tracks
  62. 62. Annotation Tracks
  63. 63. Annotation Tracks
  64. 64. Annotation Tracks
  65. 65. Browser graphics in PDF TABLE GET CURRENT BROWSER DNA BROWSER GRAPHIC IN PDF TO GET OTHERCLICK DATALINE
  66. 66. 1 CURRENT BROWSER GRAPHIC IN PDFTO GETOTHER DATA
  67. 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. 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. 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. 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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