Genome Browsers And Genome Databases. Andy Conley Computational Genomics 2009

Transcription

1 Genome Browsers And Genome Databases Andy Conley Computational

2 What is a Genome Browser Genome browsers facilitate genomic analysis by presenting alignment, experimental and annotation data in the context of genomic DNA sequences. Melissa S Cline & James W Kent,

3 Current Browsers There are a number of genome browser platforms are out there. UCSC, ensembl, NCBI, JGI, GBrowse Cline, M. S. and W. J. Kent (2009). "Understanding genome browsing." Nat Biotechnol 27(2): ^^ Covers mainly just the UCSC genome browser. 3

4 UCSC Genome Browser Huge, very functional. Contains many, many genomes. Lots of additional tools, e.g. table browsing. UCSC Genome Browser 4

5 GBrowse Generic Genome Browser Part of GMOD Free, open source Flexible Widely used (60+ projects) 5

6 WormBase Database of various Caenorhabditis genomes and other nematodes (little worm things). Uses GBrowse as it s genome viewer. One of the more mature GMOD installations. WormBase 6

7 FlyBase Another (perhaps the most) mature GMOD installation. Home to the genomes of 12 Dropsophila genomes currently. FlyBase 7

8 NeisseriaBase Our version of GBrowse. Contains our four strains of N.meningitidis from last year. Also includes four previously sequenced strains and two N.gonorrhea strains. 8

9 What do they all have in common? All of these browsers look different, have different organisms, etc. They all do one important thing: they combine different sources of data. They also present the data in an easy to access format. 9

10 Functionality of a Browser What does the browser do in terms of our data? Allow navigation of the genome Show features Show annotations Show comparisons 10

11 Tracks What are tracks? Tracks are data! 11

12 More Tracks Genes: generally the most important track. You also have ESTs and mrnas. You have expression tracks. 12

13 WormBase, FlyBase and ToxoDB FlyBase WormBase ToxoDB 13

14 Looking Around in NeisseriaBase 14

15 Functional Annotation Looking at genes is great, but we want more information about them. When you click on a feature, gene, trna, etc., you want to learn more about it. This is the core of the browser functionality. 15

16 UCSC The UCSC genome browser integrates a lot of information for a given gene. GABRA3 on the UCSC Browser 16

17 FlyBase & WormBase FlyBase shows even more information than the UCSC browser. Dmel\cnn on FlyBase K04D7 on WormBase 17

18 NeisseriaBase We have integrated a decent amount of functional and comparative information into NeisseriaBase D-Amnio Acid Dehydrogenase 18

19 Comparative Genomics Other major source of data in a browser. The whole reason to sequence different closely related species is to compare them. 19

20 Conservation What parts of the genomes are conserved across species? What parts of the genomes are syntenic across species? What genes are present or absent across species? 20

21 Comparative Genomics in the UCSC Browser Conservation on a base-level Aligned regions. Conserved coding sequences UCSC Genome Browser 21

22 WormBase WormBase provides alignments of C.briggsae to the C.elegans genome, and vice-versa. Alignments of ESTs from other species to the genomes. dev.wormbase.org had more. 22

23 FlyBase Provides alignments of other organisms to the Drosophila species. Also has a list of orthologs for each gene. 23

24 Synteny The ordering of features in the genome. Genomes, bacterial ones in particular, are fluid. The ordering can change over time. Synteny comparison can tell you about the evolution of the organisms genome. 24

25 Gbrowse_syn A synteny viewer based off of GBrowse. Allows the display of syntenic regions and the features in them. WormBase s GBrowse_syn is down and FlyBase hasn t implemented it yet. The Pseudomonas genome database does have GBrowse_syn implemented. 25

26 WormBase 26

27 Is a Browser Useful? 27

28 Volumes of Data We deal with huge volumes of data. We want things to be high throughput. We want to analyze. A genome browser does none of this. 28

29 So why make one? Not everybody cares about high throughput. A lot of wet-lab biologists have never heard of PERL. They may have only a few genes of interest that they study experimentally. A genome browser provides a way for them to easily access information. Thalassiosira pseudonana 29

30 We Still Need Browsers It always helps to see your data. Browsers help you make sure your data are correct. Plus, they make pretty pictures. 30

31 In Summary The Purpose of a Browser is to: Visualize data Provide annotations for the data Show comparative genomics Be useable for non-programmers. 31