JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

doi:10.1186/1471-2105-9-177

BMC Bioinformatics

Volume 9

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Richter M
Lombardot T
Kostadinov I
Kottmann R
Duhaime MB
Peplies J
Glöckner FO

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Lombardot T
Kostadinov I
Kottmann R
Duhaime MB
Peplies J
Glöckner FO
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JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

Michael Richter¹^,2 , Thierry Lombardot¹ , Ivaylo Kostadinov¹^,2 , Renzo Kottmann¹^,2 , Melissa Beth Duhaime¹^,2 , Jörg Peplies³ and Frank Oliver Glöckner¹^,2

¹Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany

²Jacobs University Bremen gGmbH, D-28759 Bremen, Germany

³Ribocon GmbH D-28359 Bremen, Germany

author email corresponding author email

BMC Bioinformatics 2008, 9:177doi:10.1186/1471-2105-9-177


Published:	1 April 2008

Abstract

Background

Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.

Results

The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets.

Conclusion

JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.