UCSC Genome Browser 1

The Progress 2

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 Nucleic Acids Research has grown exponentially 2009: 1170 databases and tools

NCBI Map Viewer EBI Ensembl Genome Browsers 4 UCSC Genome Browser

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

Ensembl: 6

Ensembl – Human Y chromosome 7

NCBI Map Viewer 8 National Center for Biotechnology Information (NIH)

UCSC Genome Browser: genome.ucsc.edu 9

UCSC Genome Browser 10

Organization of genomic data… 11 Genome backbone: base position number sequence Annotation Tracks chromosome band known genes predicted genes evolutionary conservation SNPs sts sites gap locations repeated regions microarray/expression data more… Links out to more data

A sample of what we can find: 12 gene details comparisons SNPs Annotation Tracks official sequence

The Genome Browser Gateway start page, basic search Use this Gateway to search by: ◦ Gene names, symbols ◦ Chromosome number: chr7, or region: chr11: ◦ Keywords: kinase, receptor ◦ IDs: NP, NM, OMIM, and more… See lower part of page for help with format 13 text/ID searches

The Genome Browser Gateway start page choices, December 2006 Make your Gateway choices: 1. Select Clade 2. Select species: search 1 species at a time 3. Assembly: the official backbone DNA sequence 4. Position: location in the genome to examine 5. Image width: how many pixels in display window; 5000 max 6. Configure: make fonts bigger + other choices

15 The Genome Browser Gateway sample search for Human TP53 Sample search: human, March 2006 assembly, tp53 select Select from results list ID search may go right to a viewer page, if unique

16 Overview of the whole Genome 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

17 Sample Genome Viewer image, TP53 region base position STS markers Known genes RefSeq genes GenBank seqs repeats 17 species compared SNPs single species compared

18 Visual Cues on the Genome Browser 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 Tick marks; a single location (STS, SNP) Intron, and direction of transcription >> < exon < < << < ex 5' UTR3' UTR For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track)

19 Options for Changing Images: Upper Section 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 fonts, window, more Walk left or right Zoom in Zoom out click to zoom 3x and re-center

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

21 Annotation Track options, defined Hide: 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

22 Reset, Hide, Configure or Refresh to change settings You control the views Use pulldown menus Configure options page reset, back to defaults start from scratch enforce any changes (hide, full, squish…)

23 Click 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

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

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

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

27 Accessing the BLAT tool BLAT = BLAST-like Alignment Tool

28 BLAT tool overview: Make choices DNA limit bases Protein limit aa 25 total sequences Paste one or more sequences

29 BLAT results, with links go to browser/viewergo to alignment detail

30 BLAT results, browser link

31 BLAT results, alignment details

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

33 In-Silico PCR: Find genomic sequence using primers