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DMDM: Domain Mapping of Disease Mutations

Overview
Journal Bioinformatics
Specialty Biology
Date 2010 Aug 6
PMID 20685956
Citations 35
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Abstract

Unlabelled: Domain mapping of disease mutations (DMDM) is a database in which each disease mutation can be displayed by its gene, protein or domain location. DMDM provides a unique domain-level view where all human coding mutations are mapped on the protein domain. To build DMDM, all human proteins were aligned to a database of conserved protein domains using a Hidden Markov Model-based sequence alignment tool (HMMer). The resulting protein-domain alignments were used to provide a domain location for all available human disease mutations and polymorphisms. The number of disease mutations and polymorphisms in each domain position are displayed alongside other relevant functional information (e.g. the binding and catalytic activity of the site and the conservation of that domain location). DMDM's protein domain view highlights molecular relationships among mutations from different diseases that might not be clearly observed with traditional gene-centric visualization tools.

Availability: Freely available at http://bioinf.umbc.edu/dmdm.

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References
1.
Murzin A, Brenner S, Hubbard T, Chothia C . SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536-40. DOI: 10.1006/jmbi.1995.0159. View

2.
McKusick V . Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet. 2007; 80(4):588-604. PMC: 1852721. DOI: 10.1086/514346. View

3.
Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

4.
Pruitt K, Tatusova T, Maglott D . NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2006; 35(Database issue):D61-5. PMC: 1716718. DOI: 10.1093/nar/gkl842. View

5.
Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View