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Brief Bioinform. 2013 Mar;14(2):131-43. doi: 10.1093/bib/bbs029. Epub 2012 Jul 3.

A brief introduction to web-based genome browsers.

Author information

1
College of Life Sciences, Peking University, Beijing 100871, P.R. China.

Abstract

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.

PMID:
22764121
DOI:
10.1093/bib/bbs029
[Indexed for MEDLINE]

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