MutDB.org was originally developed and designed at Stanford University by Sean Mooney, PhD. This new version was developed by Jessica Dantzer at the Center for Computational Biology and Bioinformatics, part of the Indiana University School of Medicine's Department of Medical and Molecular Genetics. In addition, the SNP Selection tool was developed by Adebayo Olowoyeye, and the KEGG pathway visualizations were developed by Arti Singh. This work was funded by the Ronald E. McNair Fellowship program and the Showalter Trust. Questions? Contact Jessica Dantzer or Sean Mooney
Updates
2007-02-06
New: SNP Browser SNP selection tool
New: KEGG gene pathways, linked via gene pages
Updated to dbSNP build 126
Updated to Swiss-Prot release 51
006-01-05
Added SIFT prediction scores for each nonsynonymous SNP or mutation
Added searches by specific SNP identifiers
Added search bar to title bar of index, gene, and SNP pages
2005-10-11
Updated to Swiss-Prot release 45
Added SNP color-coding and conservation tracks to SNP-to-gene maps
2005-09-06
Added intronic SNPs and untranslated mRNA SNPs to associated gene pages
Added new gene page navigational links
Updated to dbSNP build 124
Added more complete set of mapped structures
Data Retrieval
The single nucleotide polymorphism (SNP) and mutation data in MutDB is taken from two
publicly available databases, Swiss-Prot and dbSNP. The flat files
containing the data housed in these databases were downloaded to a local
machine, then parsed using Perl, using BioPerl libraries. The data will continue to be updated as new versions of the Swiss-Prot and dbSNP databases become available.
For each gene containing SNPs and mutations, associated protein structures have been found. Using the protein sequences recorded from the Swiss-Prot and NCBI databases, a BLAST search is performed against the PDB for both the wild type and mutant
amino acid strains. Results from these searches are kept only if they
are identical to the query sequence. Local
copies of the PDB files are then used to find the exact matches within the protein sequence, using pattern matching and pairwise alignments.
The conservation tracks on each SNP-to-gene map were created from data existing in the UCSC Human Genome data. Conservation scores for each nucleotide position, organized by chromosome, were downloaded to a local machine, and an average was calculated over every twenty positions. The averages are used to create the graph displayed on each image.
The purpose of this resource is to distribute functional annotations of mutation data. These mutations are meant to be used for basic research. Do not use these mutations to make clinical decisions. The annotations may be freely downloaded and used for non-commercial use as long as MutDB.org is properly cited. The underlying mutation data is derived from other sources such as dbSNP and Swiss-Prot. Any use of the underlying mutation data may be subject to restrictions. Please inquire with the source data provider (linked on every mutation annotation page) for more information.
