Genome Browser. Background & Strategy. Spring 2017 Faction II

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1 Genome Browser Background & Strategy Spring 2017 Faction II

2 Outline Beginning of the Last Phase Goals State of Art Applicable Genome Browsers Not So Genome Browsers Storing Data Strategy for the website Website Structure Genome Visualization Extended Tools & Features

3 Outcome of each Group

4 As we approach the Last Phase

5 Goals

6 State of the Art Overview: Provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks. Stacks annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. User can look at a whole chromosome to get a feel for gene density. Open a specific cytogenetic band to see a positionally mapped disease gene candidate. Zoom in to a particular gene to view its features. Other links tie the Genome Browser to the BLAT alignment tool, provide access to the underlying relational database via the Table Browser, convert coordinates across different assembly date, etc

7 Applicable Genome Browsers

8 Released in 2009

9 General Features

10 Architecture

11 JBrowse A fast, embeddable genome browser Technical summary: Programming language Built completely with JavaScript and HTML5 Optional run-once data formatting tools written in Perl. Server-side code, no back-end server code. Very light server resource requirements. Web-service and stand-alone application Desktop application for MacOX and Windows, Docker Image is available Latest release JBrowse release

12 JBrowse Headline Features Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Includes an optional faceted track selector suitable for large installations with thousands of tracks. Supported input GFF3, FASTA, Wiggle, BED, REST, and more. BigWig, BAM, VCF (with tabix) Frontend, Better picture quality and UI; Lightweight, easy to implement; Not requiring a database to store the gff files

13 JBrowse

14 Biodalliance

15 Fast, embeddable genome visualization Track-oriented genome viewer HTML5 web standards Add data DAS, Distributed Annotation System Direct access to a range of standard genomic file formats

16 Navigation Several distinct tracks of information about the genome Gene structures, are fetched from servers operated as part of the Dalliance project Others from, for instance, the chromatin segmentation track comes from the ENCODE

17 Navigation zoom in far enough to see the base-pair-level genome sequence

18 Searching Type, then highlighted

19 Leaping Some track types support rapid movement between features

20 Customizing tracks customize tracks by selecting and clicking change the order of tracks by dragging and dropping

21 Embedding Dalliance is a self-contained Javascript object which can be inserted into almost any web page

22 GenoVerse A portable, customizable, back-end independent JavaScript and HTML5 based genome browser. Genoverse works with a variety of formats, such as XML, JSON, GFF, GFF3, BED. Local files can simply be dragged and dropped directly onto Genoverse from the file manager, which will trigger the parsing of the data within the browser, and visualize it as a new track without uploading the file online.

23 Visual Interface:

24 Genome Projector Language: Perl, Asynchronous JavaScript and XML (AJAX) technology. -Uses Google Maps API Genome Visualization features: zoomable user interface with multiple views: 1. Circular Genome Map View 2. Genome Map View 3. Biochemical Pathway Map View 4. DNA Walk Map View Input File Format: -Gbk files for generating all views Last Release: 2016/01/04

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31 Not so Genome Browsers D3 Browser Rgb Browser Gaggle GenPlay WebApollo Circos (Static Images) NGS-Gen Browser (Matlab based) GenomeSavant (Desktop application) GenomeVito (Desktop application)

32 D3 Browser Pros: Incredibly flexible as a result of being a generalist tool Looks great Cons: Requires a lot of work, as it is only a generally visualization tool No built in tools for handling file parsing and uses data in JSON format Coding require for basic features likes viewing information on click, viewing list of contigs, etc. Feasibility: Proportional to invested effort

33 R Genome Browser (Rgb) A R package that can create a simple genome browser. Building track: Usual annotation tracks (download from UCSC/NCBI, eg. GTF file, track.exons.ccds, track.cnv.dgv,track.genes.ncbi, track.bands.ucsc) Custom annotation tracks Next Generation Sequencing tracks (bam file) Pros: Open-source licensing Support various operating system ports Offers an object-oriented framework Flexible (have GUI for R beginner) Cons: Time-consuming High memory usage

34 Gaggle Pros: Great for overlaying different data :Chipseq, Tiling Arrays, high throughput data Modular and can be extended with other components from the Gaggle Framework Can display transcriptome information in the form of a network Cons: Very Sparse Documentation Dependencies somewhat obsolete Almost entirely Local Feasibility: Low

35 GenPlay

36 WebApollo

37 Storing Genome Data in Server

38 Storage Different genome browsers can use different storage methods like: Relational databases (MySQL) Flat file system Non-Relational Databases

39 Try to keep maximum file types fastq GeneBank GFF3 Fasta

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41 Website Structure

42 Extended Tools and Features w

43 References

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