Transcript Document
Genome Browsers Carsten O. Daub Omics Science Center RIKEN, Japan May 2008 Outline • Give some impression of the intuitive handling of the browsers • Highlight some of the specific functions • Point out some of the strengths of the different browsers General comments • We will focus on two genome growsers in this lecture • UCSC genome browser • ENSEMBL genome browser • Some comments about the RIKEN FANTOM3 genome browser General comments cont’d. • The genome browsers are parts of bigger genome information resources • Their main purpose is to graphically display complex information • And to put this information into the genomic context • We will not discuss all of the rich functionalities of UCSC and ENSEMBL here General comments cont’d. • Genome browsers are tools to – display various types of information – in the context of the genome The context of the genome • Graphical representation of the genome • The chromosomes are displayed as straight ’strings’ • With coordinates for the positions • Various features are aliged to the chromosomes and displayed as tracks What information is displayed? • Which features can be displayed in such a way? • Which features NOT? UCSC genome browser chr7 Mouseover effect Zoom in Tracks Comments on Gene models Some comments on gene models: • different databases have different ways to define gene models Common examples are • NCBI: RefSeq, ’Known genes’ • ENSEMBL: Known genes, Novel genes, Predicted genes • What are the differences of the models? • Which one is the better model? stat3 Tracks in the Genome Browser • Various types of information are aligned to the genome in groups, so calles tracks • Each track contains a logical unit of information – Different gene models – Experimental evidence: cDNA, mRNA, EST – Expression and regulation – Repeats, SNPs, miRNA, ... – Comparative genomics Customizing tracks • Tracks can be displayed in different levels of detail dense FULL Upload your own track • You can upload your own track to the genome browser – As a file – As a URL pointing to a file – Data must be formatted in BED, GFF, GTF, WIG or PSL formats. • Example: – You want to display miRNA target predictions in the genome browser Export as high quality graphic • It can be important, for example for a publication, to obtain high quality versions of the graphs displayed in the genome browser Customizing the display • Many details about the display can be customized UCSC genome browser as data repository • The genome browser is the front-end of a data repository • The backend is a database that contains all the details about the displayed information • The information in the databases can be retrieved seperately from the download section ENSEMBL • About the Ensembl Project • Ensembl is a joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. • Goals of Ensembl • The Ensembl project aims to provide: • Accurate, automatic analysis of genome data. • Analysis and annotation maintained on the current data. • Presentation of the analysis to all via the web. • Distribution of the analysis to other bioinformatics laboratories. stat3 Summary • The UCSC browser and the ENSEMBL browser have very similar functions • It needs some time to get accustomed to any of them • Remommendation: – Choose one of them – Get used to it – Stick to it Summary cont’d • They are highly flexible • They allow to easily get an impression of a genomic region • They are extremely powerful tools for – beginners as well as for experts – For biologists as well as Bioinformaticians RIKEN Genomic Elements Viewer • RIKEN provides the genomic elements viewer • It was specifically developed to display the RIKEN CAGE data • CAGE data provides infoemation about the start of a transcript • And is very valuable for e.g. – Promoter analysis – Alternative regulation (isoforms)