Abstract
The identification of regulatory regions for a gene is an important step towards deciphering the gene regulation. Regulatory regions tend to be conserved under evolution that facilitates the application of comparative genomics to identify such regions. The present study is an attempt to make use of this attribute to identify regulatory regions in the Mycobacterium species followed by the development of a database, MycoRRdb. It consist the regulatory regions identified within the intergenic distances of 25 mycobacterial species. MycoRRdb allows to retrieve the identified intergenic regulatory elements in the mycobacterial genomes. In addition to the predicted motifs, it also allows user to retrieve the Reciprocal Best BLAST Hits across the mycobacterial genomes. It is a useful resource to understand the transcriptional regulatory mechanism of mycobacterial species. This database is first of its kind which specifically addresses cis-regulatory regions and also comprehensive to the mycobacterial species. Database URL: http://mycorrdb.uohbif.in.
Highlights
Over the past few years the genomic sequence repertoire of mycobacterial sequences has increased tremendously
Our present study addresses this issue, as it identifies the putative cis- regulatory sequences within the intergenic regions of mycobacterial species and the similar DNA motif in a genome
Our study began with the identification of the Reciprocal Best BLAST Hits (RBBHs) which serves as potential ortholog
Summary
Over the past few years the genomic sequence repertoire of mycobacterial sequences has increased tremendously. One of the important aspects to compare genome sequences is to find orthologous proteins among the existing species [2,3]. The identification of orthologs is important to assist the functional annotation of a gene and to identify its regulatory region. These regions are known to evolve at a slower rate than non-functional elements, and finding the conserved DNA motifs within non coding region is an efficient method to predict these regions [4,5]. Different approaches have been used to find the regulatory regions [6–8]. Identification of these DNA elements relies on an extensive set of known target genes [4,9]. Identification of regulatory region for a novel transcriptional regulator remains a challenging task
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