MycoRRdb: a database of computationally identified regulatory regions within intergenic sequences in mycobacterial genomes.

PloS One
Mohit MidhaVaibhav Vindal

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.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 1, 1994·Molecular Microbiology·S Bergh, S T Cole
Mar 9, 2000·Tubercle and Lung Disease : the Official Journal of the International Union Against Tuberculosis and Lung Disease·G M RodriguezI Smith
Jan 3, 2001·Nature Medicine·D B Young
Mar 27, 2002·Journal of Bacteriology·Shelley E HaydelJosephine E Clark-Curtiss
Sep 2, 2003·Journal of Bacteriology·Claudia SalaDaniela Ghisotti
Feb 16, 2006·PLoS Computational Biology·Rahul SiddharthanErik van Nimwegen
May 30, 2006·BMC Bioinformatics·Debra L FultonFiona S L Brinkman
Jul 18, 2006·Nucleic Acids Research·Timothy L BaileyWilfred W Li
Dec 16, 2006·Nucleic Acids Research·Phuongan DamYing Xu
Nov 29, 2007·Bioinformatics·Gabriel Moreno-Hagelsieb, Kristen Latimer
Jul 17, 2008·Comparative and Functional Genomics·Graham R StewartDouglas B Young
Aug 7, 2008·BMC Genomics·Anchal VishnoiAlok Bhattacharya
Oct 7, 2008·Nucleic Acids Research·T B K ReddyGary K Schoolnik
Nov 8, 2008·Nucleic Acids Research·Fenglou MaoYing Xu
Dec 21, 2010·Molecular Microbiology·Richard A FestaK Heran Darwin

❮ Previous
Next ❯

Citations

Oct 12, 2012·Bioinformation·Mohit MidhaVaibhav Vindal
Apr 29, 2015·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Raja PolavarapuVaibhav Vindal
Jun 1, 2016·Frontiers in Microbiology·Ghanshyam S YadavPradip K Chakraborti

❮ Previous
Next ❯

Software Mentioned

MycoRRdb
MEME
BLASTP

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.