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MGDD: Mycobacterium tuberculosis Genome Divergence Database

BACKGROUND: Variation in genomes among different closely-related organisms can be linked to phenotypic differences. A number of mechanisms, such as replication error, repeat expansion and contraction, recombination and transposition can contribute to genomic differences. These processes lead to gene...

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Detalles Bibliográficos
Autores principales: Vishnoi, Anchal, Srivastava, Alok, Roy, Rahul, Bhattacharya, Alok
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518163/
https://www.ncbi.nlm.nih.gov/pubmed/18681951
http://dx.doi.org/10.1186/1471-2164-9-373
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author Vishnoi, Anchal
Srivastava, Alok
Roy, Rahul
Bhattacharya, Alok
author_facet Vishnoi, Anchal
Srivastava, Alok
Roy, Rahul
Bhattacharya, Alok
author_sort Vishnoi, Anchal
collection PubMed
description BACKGROUND: Variation in genomes among different closely-related organisms can be linked to phenotypic differences. A number of mechanisms, such as replication error, repeat expansion and contraction, recombination and transposition can contribute to genomic differences. These processes lead to generation of SNPs, different types of repeat-based and transposons or IS-element-based polymorphisms, inversions and duplications and changes in synteny. A database of all the variations in a group of organisms is not only useful for understanding genotype-phenotype relationship but also in clinical applications. There is no database available at present that provides information about detailed genomic variations among different strains and species of Mycobacterium tuberculosis complex, organisms responsible for human diseases. DESCRIPTION: MGDD is a free web-based database that allows quick user friendly search to find different types of genomic variations among a group of fully sequenced organisms belonging to M. tuberculosis complex. The searches are based on data generated by pair wise comparison using a tool that has already been described. Different types of variations that can be searched are SNPs, indels, tandem repeats and divergent regions. The searches can be designed to find specific variations either in a given gene or any given location of the query genome with respect to any other genome currently available. CONCLUSION: Web-based database MGDD can help to find all the possible differences that exists between two strains or species of M. tuberculosis complex. The search tool is very user-friendly and can be used by anyone not familiar with computational methods and will be useful to both clinicians and researchers working on tuberculosis and other Mycobacterial diseases.
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spelling pubmed-25181632008-08-20 MGDD: Mycobacterium tuberculosis Genome Divergence Database Vishnoi, Anchal Srivastava, Alok Roy, Rahul Bhattacharya, Alok BMC Genomics Database BACKGROUND: Variation in genomes among different closely-related organisms can be linked to phenotypic differences. A number of mechanisms, such as replication error, repeat expansion and contraction, recombination and transposition can contribute to genomic differences. These processes lead to generation of SNPs, different types of repeat-based and transposons or IS-element-based polymorphisms, inversions and duplications and changes in synteny. A database of all the variations in a group of organisms is not only useful for understanding genotype-phenotype relationship but also in clinical applications. There is no database available at present that provides information about detailed genomic variations among different strains and species of Mycobacterium tuberculosis complex, organisms responsible for human diseases. DESCRIPTION: MGDD is a free web-based database that allows quick user friendly search to find different types of genomic variations among a group of fully sequenced organisms belonging to M. tuberculosis complex. The searches are based on data generated by pair wise comparison using a tool that has already been described. Different types of variations that can be searched are SNPs, indels, tandem repeats and divergent regions. The searches can be designed to find specific variations either in a given gene or any given location of the query genome with respect to any other genome currently available. CONCLUSION: Web-based database MGDD can help to find all the possible differences that exists between two strains or species of M. tuberculosis complex. The search tool is very user-friendly and can be used by anyone not familiar with computational methods and will be useful to both clinicians and researchers working on tuberculosis and other Mycobacterial diseases. BioMed Central 2008-08-05 /pmc/articles/PMC2518163/ /pubmed/18681951 http://dx.doi.org/10.1186/1471-2164-9-373 Text en Copyright © 2008 Vishnoi et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Vishnoi, Anchal
Srivastava, Alok
Roy, Rahul
Bhattacharya, Alok
MGDD: Mycobacterium tuberculosis Genome Divergence Database
title MGDD: Mycobacterium tuberculosis Genome Divergence Database
title_full MGDD: Mycobacterium tuberculosis Genome Divergence Database
title_fullStr MGDD: Mycobacterium tuberculosis Genome Divergence Database
title_full_unstemmed MGDD: Mycobacterium tuberculosis Genome Divergence Database
title_short MGDD: Mycobacterium tuberculosis Genome Divergence Database
title_sort mgdd: mycobacterium tuberculosis genome divergence database
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518163/
https://www.ncbi.nlm.nih.gov/pubmed/18681951
http://dx.doi.org/10.1186/1471-2164-9-373
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