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Title
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D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs |
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Authors |
Naresh Sen, Manoj Mishra, Feroz Khan*, Abha Meena, Ashok Sharma
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Affiliation
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Bioinformatics & In Silico Biology Division (BISB), Central Institute of Medicinal & Aromatic Plants (CIMAP), (Council of Scientific & Industrial Research), Lucknow-226015 (UP), India
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Article Type
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Web Server | |
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Date
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Received December 20, 2008; revised March 02, 2009; accepted April 16, 2009; published July 27, 2009
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Abstract |
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.
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Keywords |
Weight matrix, motif prediction, file format, motif databases
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Citation |
Sen et al, Bioinformation 3(10): 415-418 (2009) | |
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics | |
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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