Abstract
BackgroundCompletion 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.ResultsThis 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.ConclusionThe 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: .
Highlights
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
We have developed a web-based sequence retrieval system that quickly and extracts non-coding sequences associated with a specific user defined gene set from a single and/or multiple genomes
The Non-Coding Sequences Retrieval System (NCSRS) efficiently delivers non-coding sequences for specified genes or gene sets using a user-friendly interface from a single site
Summary
We have developed a web-based sequence retrieval system that quickly and extracts non-coding sequences associated with a specific user defined gene set from a single and/or multiple genomes. The NCSRS efficiently delivers non-coding sequences for specified genes or gene sets using a user-friendly interface from a single site This system eliminates the need to manually sift though genome sequences and look for annotation information from multiple sources. The system allows the user to specify the gene or set of genes for retrieval while maintaining a simple user interface, enabling the user to apply their expert knowledge without having to spend a lot of time learning how to use the system Another option that is important for those seeking to elucidate functional NCS is masking. It is even possible to combine the two approaches and obtain sequences for all homologous genes of a set of genes with similar expression profiles This allows for the system to be utilized by those who seek to learn more about genome-wide networks through their analysis [39]. A table with links to NCBI, UCSC genome browser and Ensembl for the gene and specific species is provided
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