Genome Browser Background and Strategy

Transcription

1 Genome Browser Background and Strategy April 12th, 2017 BIOL Faction I (Outbreak) - Genome Browser Group Adam Dabrowski Mrunal Dehankar Shareef Khalid Hubert Pan Ajay Ramakrishnan Ankit Srivastava Kris Wang Seyed Alireza Zamani

2 Overview Introduction to Genome browsers Overview of criteria for selection Exploration of candidate browsers Honorable mentions Additional features on the browser

3 What s a Genome Browser? A tool that allow you to view, analyze, and possibly edit genome data Usually consists of some sort of database coupled with frontend In this class we are going to focus primarily on web based open source browsers?

4 Model View Controller Popular paradigm for designing human facing computer programs Model holds data (kind of like basket of values) View - displays the UI to the user Controller handles the interaction with the user by changing the model and the view ml

5 Selection Notes We are using CompaGB as a foundation that presents a wide range of criteria As we go further into the process, and continually analyze each browser we are updating our list of criteria to match our necessities to fit the task at hand

6 Selection Criteria Generic Stability Documentation & ease of use Code modifications & extensions Data Content & Connectivity Export and import annotation to and from local files Comparative Genomics Search abilities By annotation Genome location Similarity to a query sequence Navigation Pan Zoom Ease of Setup User Interface Color, User Design Performance Time taken on startup Response time for data loading and display Disk space on installment

7 Candidate Genome Browsers

8 Integrative Genomics Viewer (IGV) Lightweight HTML5 version of the desktop browser from Broad Institute First released in June 2016; most recent release on February 28th Written in JavaScript and CSS Supports a wide variety of file formats (e.g. FASTA, GFF, VCF, etc.) Pros Dynamic loading of multiple tracks Customizable tracks Searching for a gene or a locus Smooth zooming and panning Cons ⅹ ⅹ ⅹ Doesn t support context menus Relatively new, not widely used Not very aesthetically pleasing

9 Genome Maps HTML5 web-based genome browser: Written in JavaScript and CSS3 Supports a wide variety of file formats (e.g. BAM, VCF,...) Fetching data from CellBase Pros Dynamic loading of multiple tracks Searching for a gene or a locus Nucleotide level detail Designed to be easily embedded in other bioinformatics projects. ⅹ ⅹ ⅹ Slow with DAS servers Poor documentation No new update since 2013 Cons Nucleic Acids Res. 2013;41(W1):W41-W46. doi: /nar/gkt Tool bar Region overview Region in detail

10 JBrowse Setup Browser built on HTML5 and Javascript Uses AJAX Pros Lightweight, fast and embeddable Can scale to large amounts of data Multiple input types Quantitative tracks can be displayed Out of the box search feature Cons ⅹ Write once

11 UCSC Genome Browser Widely perceived as one of the more feature filled genome browsers. Perceived as difficult to install Pros Cons х Does pretty much everything that the rest of the tools do Possibly difficult to install

12 BLAT Blast Like Alignment Tool Allows for navigation by sequence similarity

13 In Silico PCR Allows end users to find out what other sequence segments may be excised for a given Primer Pair This may be useful when attempting to extract a target sequence for wet lab experiments.

14 Strand NGS Pros: Contains an elastic feature that shows multiple genomic regions simultaneously Color coded results based on if mates are missing, too far or on different chromosomes Presents a histogram with mismatch lists Cons: х Not dynamic х Does not annotate х Debatably not public (still waiting for confirmation)

15 Genome Savant Built on Java and desktop based Pros: Allows functionality to be added through custom plugins Dynamic Allows SNP visualization for population studies. Easy to view structural variations Con: х Dependent on reference Genomes, which we don t have

16 pileup.js Browser based genome viewer Inspirations: IGV, Biodalliance Pros: Well documented Transition from SVG to HTML5 canvas Enables consistent state changes User-defined sources for data loading schemes Supports context menus Credits: Vanderkam et al. pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data

17 Honorable Mentions

18 Artemis Geared towards Displaying NGS data

19 String DB Visual Network Analysis of Protein Interactions oowhsnjfoq7 More Lines = More Evidence Different Colors = Different Evidence types

20 Bonus Features Blast (virulence Profiler) + Phylogenetic tree + Geographic locations of outbreaks

21 Citations Zweig, Ann S. et al. UCSC Genome Browser Tutorial. Genomics 92.2 (2008): ScienceDirect. Web. UCSC Genome Browser Home. N.p., n.d. Web. 12 Apr Robinson, James T., et al. "Integrative genomics viewer." Nature biotechnology 29.1 (2011): Igv.js Fiume M. et al. (2012) Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res., 40, W615 W621 Medina, Ignacio, et al. "Genome Maps, a new generation genome browser." Nucleic acids research 41.W1 (2013): W41-W46. Skinner, M. E., A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes. "JBrowse: A next-generation genome browser."genome Research19.9 (2009): Web. Vanderkam D. et al. pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data Bioinformatics 32(15) (2016):