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PairWise Neighbours database: overlaps and spacers among prokaryote genomes
Albert Pallejà1, Tomàs Reverter, Santiago Garcia-Vallvé
1Department of Biochemistry and Biotechnology, Rovira i Virgili University, Tarragona, Catalunya, Spain. albert.palleja@urv.cat
BMC Genomics
|June 27, 2009
Summary
The PairWise Neighbours database analyzes gene overlaps and spacers in prokaryotes, aiding in accurate translation initiation site annotation. This resource helps validate gene structures and Shine-Dalgarno sequences for improved genomic analysis.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Prokaryotic genomes share common architectural features, including overlapping genes and short intergenic spacers.
- Short overlaps minimize mutation risks, while short spacers conserve non-coding DNA.
- Essential regulatory signals, like the Shine-Dalgarno (SD) sequence for translation, necessitate minimal spacer length.
Purpose of the Study:
- To develop and present the PairWise Neighbours database for analyzing gene overlaps and spacers in prokaryotes.
- To provide a resource for studying the conservation and characteristics of these genomic features across species.
- To facilitate the analysis of intergenic regions, including the identification and strength of SD sequences.
Main Methods:
- Developed the PairWise Neighbours database, an interactive tool for prokaryotic genome analysis.
- Compiled data from 678 fully sequenced prokaryote genomes, encompassing 1,956,294 gene pairs.
- Integrated features for analyzing gene overlaps, spacer lengths, and SD sequence properties.
Main Results:
- The PairWise Neighbours database provides comprehensive information on gene overlaps and spacers.
- It offers insights into the conservation of these features across bacterial and archaeal species.
- The database allows detailed analysis of intergenic regions, including SD sequence location and strength.
Conclusions:
- A database for studying prokaryotic gene overlaps and spacers is valuable for genomic research.
- PairWise Neighbours aids in the reliability analysis of overlapping gene structures.
- The database assists in validating gene initiation site annotations by examining SD sequence presence and location.
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