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About MutDB

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.

A more complete description of annotation procedures can be found in Dantzer, Moad, Heiland and Mooney, Nucleic Acids Research (2005). This was previously published in Mooney and Altman (2003).

Conservation Tracks and SIFT Scores

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.

In addition, SIFT, http://blocks.fhcrc.org/sift/SIFT.html, software was generously provided by Pauline Ng, Ph.D.

Supported By

The work is funded by:
  • NIH K22LM009135 (PI: Mooney)
  • NIH 1R01LM009722 (PI: Mooney)
  • Indiana Genomics Initiative. The Indiana Genomics Initiative (INGEN) is supported in part by Lily Endowment.
  • National Science Foundation, DBI‐0644017 (PI: Predrag Radivojac)

Acknowledgements

MutDB uses:

This resource is powered by:

  • Linux
  • MySql
  • Perl & BioPerl
  • Apache

We would like to acknowledge:

  • Shoji Ichikawa, Indiana University
  • Somying Promso, Indiana University
  • Russ Altman, Stanford University
  • Teri Klein, Stanford University
  • Burr Fontaine, Washington University, St. Louis
  • Scientific Data Analysis Lab, Indiana University

Disclaimer

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.

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