A Promoter Database of E-coli

EcoPromdb: A Transcriptional Regulatory Network and Promoter Database of E-coli

Anuraj Nayarisseri1, Anushka Bhrdwaj2, Khushboo Sharma3, Dhananjay Raje3and Sanjeev Kumar Singh1

  1. Bioinformatics Research Laboratory, LeGene Biosciences,91, Sector - A, Mahalakshmi Nagar, Indore, India - 452010. .
  2. In silico Research Laboratory, Eminent Biosciences, 91, Sector - A, Mahalakshmi Nagar, Indore, India - 452010.
  3. Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003, Tamil Nadu, India.

ABSTRACT

EcoPromdb is a curated database of the transcriptional regulatory network corresponding to Escherichia coli K12. Accurate and versatile information of transcriptional regulatory elements are mandatory to understand the gene regulatory mechanisms. One of the challenges of Functional Genomics is that; the identification of all the elements that take part in an organism’s transcriptional regulatory network. It is expedient to understand how the cell reacts to environmental stimuli at the level of transcriptional regulation. Escherichia coli is considered by many to be a model organism for study, due to its amenability to growth in a laboratory and the existence of closely related pathogenic and non-pathogenic strains. Present investigation identifies more accurate and potential promoter regions and operons of Escherichia coli K12. We have included biological events taking place sequentially in computational frame to evaluate the Promoters referring the existing E-coli genomic repositories like Regulondb, Ecocyc, EcoGene etc. Many E-Coli Genome databases are available for such studies. However, most of them are only dedicated to either Promoter annotation or transcription factor binding and functional information, which make data access disconnected and correlation. Hence, here we introduce a promoter database for E Coli K12 which can be very useful for future research community who works on E-coli gene regulation. In current research total 2831 promoters have been discovered using Perl program from the upstream integenic region referring each operon with the TSS and terminator of E.coli k12 Genome. Database has been implemented using MySQL,Perl, PHP and Java. A very user-friendly GUI was designed using HTML, CSS, PHP and dHTML. User can search promoters, Operons, TSS and CDS corresponding to specific gene of interest from EcoPromdb using searching tools made available in Java. User can also compare the promoters with EcoPromdb using Blast algorithm which is made available in Java. The database is freely available at www.ecoprom.eminentbio.com.

Keywords: Escherichia coli, E.coli Promoter Database, E.coli K12 Promoters, E.coli gene regulation.

A Complete Genomic Repository & Transcriptional Regulatory Network of E.coli Developed at EMBS