Here we show the distribution of spacers between adjacent genes and the overlapping genes among the 678 prokaryote genomes fully sequenced. Prokaryote chromosomes contain protein-coding genes, structural RNAs and spacers between genes which are thought to typically contain regulatory signals [1]. One regulatory sequence is the Shine-Dalgarno sequence that is involved in the translation initiation process [2]. Although the ribosome does not need a perfect distance between the SD and the initiation codon [3], it is known that when the SD resides within the 4 nucleotides from the initiation codon or when is located as far as 13 nucleotides from the initiation codon, gene expression is decreased drastically [4]. In this database we provide information to asses how the SD sequence could affect the spacing lengths between adjacent genes. Another consistent feature of the prokaryote genomes is the overlapping genes [5]. Although they were originally discovered in viruses, mitochondria and other extra chromosomal nuclear elements, thousands of overlapping gene pairs have been predicted in all three transcriptional directional classes (co-directional (->->), convergent (-><-) and divergent (<-->) among the fully sequenced prokaryote genomes [6-9]. The overlapping gene pairs are higher conserved that the non-overlapping gene pairs [10]. In this database is possible to analyse the conservation of the overlaps across the species and the SD location between these gene pairs.

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Further information
If you make use of the data presented here, please cite the following articles in addition to the primary data sources:
» PairWise Neighbours database: overlaps and spacers among prokaryote genomes
Albert Pallejà, Tomàs Reverter, Santiago Garcia-Vallvé, Antoni Romeu
BMC Genomics 2009, 10:281 (25 June 2009)