Bioinformatic Databases and Tools
DbMDR: a relational database for multidrug resistance genes as potential drug targets.
Summary
DbMDR is non-redundant reference database of multidrug resistance (MDR) genes and their orthologs acting as potential drug targets. Drug resistance is a common phenomenon of pathogens, creating a serious problem of inactivation of drugs and antibiotics resulting in occurrence of diseases. Apart from other factors, the MDR genes present in pathogens are shown to be responsible for multidrug resistance. Much of the unorganized information on MDR genes is scattered across the literature and other web resources. Thus, consolidation of such knowledge about MDR genes into one database will make the drug discovery research more efficient. Mining of text for MDR genes has resulted into a large number of publications but in scattered and unorganized form. This information was compiled into a database, which enables a user not only to look at a particular MDR gene but also to find out putative homologs based on sequence similarity, conserved domains, and motifs in proteins encoded by MDR genes more efficiently. At present, DbMDR database contains 2843 MDR genes characterized experimentally as well as functionally annotated with cross-referencing search support. The DbMDR database (http://203.190.147.116/dbmdr/) is a comprehensive resource for comparative study focused on MDR genes and metabolic pathway efflux pumps and intended to provide a platform for researchers for further research in drug resistance.
AVAILABILITY:
CSIR-CIMAP server (http://203.190.147.116/dbmdr/),
CSIR-Informatics Portal (http://info.csir.res.in/data.php)
Please cite: Gupta S, Mishra M, Sen N, Parihar R, Dwivedi GR, Khan F, Sharma A. DbMDR: a relational database for multidrug resistance genes as potential drug targets. Chem Biol Drug Des. 2011 Oct;78(4):734-8.
D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.
Summary
Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network.
AVAILABILITY:
CSIR-CIMAP server (http://203.190.147.116/dmatrix/),
CSIR-Informatics Portal (http://info.csir.res.in/smisc.php)
Please cite: Sen N, Mishra M, Khan F, Meena A, Sharma A. D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs. Bioinformation. 2009 Jul 27;3(10):415-8.