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Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements

Sung Tae Doh1, Yunyu Zhang2, Matthew H Temple2 and Li Cai1*

Author Affiliations

1 Biomedical Engineering Department, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA

2 Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA

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BMC Bioinformatics 2007, 8:94  doi:10.1186/1471-2105-8-94

Published: 15 March 2007

Abstract

Background

Completion of the human genome sequence along with other species allows for greater understanding of the biochemical mechanisms and processes that govern healthy as well as diseased states. The large size of the genome sequences has made them difficult to study using traditional methods. There are many studies focusing on the protein coding sequences, however, not much is known about the function of non-coding regions of the genome. It has been demonstrated that parts of the non-coding region play a critical role as gene regulatory elements. Enhancers that regulate transcription processes have been found in intergenic regions. Furthermore, it is observed that regulatory elements found in non-coding regions are highly conserved across different species. However, the analysis of these regulatory elements is not as straightforward as it may first seem. The development of a centralized resource that allows for the quick and easy retrieval of non-coding sequences from multiple species and is capable of handing multi-gene queries is critical for the analysis of non-coding sequences. Here we describe the development of a web-based non-coding sequence retrieval system.

Results

This paper presents a Non-Coding Sequences Retrieval System (NCSRS). The NCSRS is a web-based bioinformatics tool that performs fast and convenient retrieval of non-coding and coding sequences from multiple species related to a specific gene or set of genes. This tool has compiled resources from multiple sources into one easy to use and convenient web based interface. With no software installation necessary, the user needs only internet access to use this tool.

Conclusion

The unique features of this tool will be very helpful for those studying gene regulatory elements that exist in non-coding regions. The web based application can be accessed on the internet at: http://cell.rutgers.edu/ncsrs/ webcite.