Abstract
• BackgroundAcquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome.• ResultsWe have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality.• ConclusionsOmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.
Highlights
In the late 1990s, the first fully sequenced genome of a eukaryotic organism emerged as a result of a huge community effort
We describe the development of a new open source software called OmniMapFree which can be used to enrich immediately the information available for an organism with a newly sequenced genome
The OmniMap software was developed while exploring this genome, but during development this software was tested on four other sequenced fungal genomes to ensure it retained wide species applicability
Summary
In the late 1990s, the first fully sequenced genome of a eukaryotic organism emerged as a result of a huge community effort. The annotated genome of Saccharomyces cerevisiae was subsequently published [1] and a comprehensive genome browser has gradually evolved [2,3] The success of this whole genome sequencing (WGS) project using the Sanger method, paved the way for other model species as well as industrially, agriculturally and medically important species to be nominated for WGS [4]. As a consequence early as well as later versions of genome browsers lack this wealth of additional information for the sequenced organism. Immediate access to these other data types alongside the sequenced genome would accelerate the speed of discovery, assist comparative genomic analyses and enhance the development of experimentally testable hypotheses. It is noticeable that most genome browsers operate within only a very limited range of scales, often doing best at the high magnification ranges, i.e. displaying within a single window a sequence containing < 10 contiguous genes, whilst moving between high and low scales is laborious
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