A brief introduction to web-based genome browsers

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

[1]  David Haussler,et al.  The Human Epigenome Browser at Washington University , 2011, Nature Methods.

[2]  D. Haussler,et al.  UCSC genome browser tutorial. , 2008, Genomics.

[3]  Liang Tang,et al.  Rice-Map: A new‐generation rice genome browser , 2011 .

[4]  Juancarlos Chan,et al.  WormBase: a cross-species database for comparative genomics , 2003, Nucleic Acids Res..

[5]  Qian Qian,et al.  Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice , 2010, Nature Genetics.

[6]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[7]  R. Drysdale.  FlyBase : a database for the Drosophila research community. , 2008, Methods in molecular biology.

[8]  Makoto Matsuoka,et al.  OsSPL14 promotes panicle branching and higher grain productivity in rice , 2010, Nature Genetics.

[9]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[10]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[11]  Lincoln Stein,et al.  Synbrowse: a Synteny Browser for Comparative Sequence Analysis , 2022 .

[12]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[13]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[14]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[15]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[16]  Damian Smedley,et al.  BioMart – biological queries made easy , 2009, BMC Genomics.

[17]  J. Stajich,et al.  Using the Generic Synteny Browser (GBrowse_syn) , 2010, Current protocols in bioinformatics.

[18]  Sean R. Eddy,et al.  The Distributed Annotation System , 2001, BMC Bioinformatics.

[19]  David Haussler,et al.  The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..

[20]  A Danchin,et al.  Colibri: a functional data base for the Escherichia coli genome. , 1993, Microbiological reviews.

[21]  Heinrich Magnus Manske,et al.  LookSeq: a browser-based viewer for deep sequencing data. , 2009, Genome research.

[22]  I. Dubchak,et al.  Visualizing genomes: techniques and challenges , 2010, Nature Methods.

[23]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[24]  Clifford A. Meyer,et al.  Cistrome: an integrative platform for transcriptional regulation studies , 2011, Genome Biology.

[25]  Eileen Kraemer,et al.  SynView: a GBrowse-compatible approach to visualizing comparative genome data , 2006, Bioinform..

[26]  John A. Hamilton,et al.  The TIGR Rice Genome Annotation Resource: improvements and new features , 2006, Nucleic Acids Res..

[27]  T. Wolfsberg.  Using the NCBI Map Viewer to Browse Genomic Sequence Data , 2003, Current protocols in human genetics.

[28]  Walter Gilbert,et al.  Towards a paradigm shift in biology , 1991, Nature.

[29]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[30]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[31]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2011 , 2011, Nucleic Acids Res..

[32]  Junjun Zhang,et al.  BioMart Central Portal—unified access to biological data , 2009, Nucleic Acids Res..

[33]  Andreas Prlic,et al.  Ensembl 2008 , 2007, Nucleic Acids Res..

[34]  Jean-Michel Claverie,et al.  FusionDB: a database for in-depth analysis of prokaryotic gene fusion events , 2004, Nucleic Acids Res..

[35]  Kenneth H. Fasman,et al.  The GDB human genome data base anno 1993 , 1993, Nucleic Acids Res..

[36]  Zhe Li,et al.  WebLab: a data-centric, knowledge-sharing bioinformatic platform , 2009, Nucleic Acids Res..

[37]  Ge Gao,et al.  ABrowse - a customizable next-generation genome browser framework , 2012, BMC Bioinformatics.

[38]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[39]  Lisa C. Harper,et al.  Choosing a genome browser for a Model Organism Database: surveying the Maize community , 2010, Database J. Biol. Databases Curation.

[40]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..

[41]  Masaru Tomita,et al.  Genome Projector: zoomable genome map with multiple views , 2009, BMC Bioinformatics.

[42]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[43]  Wei Zhao,et al.  Gramene: a resource for comparative grass genomics , 2002, Nucleic Acids Res..

[44]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.