Mutdb.org is dedicated to computational biology and bioinformatics
Title
MutDB
Description
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. This work was funded by the Ronald E. McNair Fellowship program and the Showalter Trust. Questions? Contact Jessica Dantzer or Sean Mooney.
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.
