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Bioinformatics. 2013 Nov 15;29(22):2953-4. doi: 10.1093/bioinformatics/btt507. Epub 2013 Sep 3.

M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci.

Author information

1
Departments of biophysics and biochemistry, University of Texas Southwestern Medical Center and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

Abstract

SUMMARY:

Online Mendelian Inheritance in Man (OMIM) is a manually curated compendium of human genetic variants and the corresponding phenotypes, mostly human diseases. Instead of directly documenting the native sequences for gene entries, OMIM links its entries to protein and DNA sequences in other databases. However, because of the existence of gene isoforms and errors in OMIM records, mapping a specific OMIM mutation to its corresponding protein sequence is not trivial. Combining computer programs and extensive manual curation of OMIM full-text descriptions and original literature, we mapped 98% of OMIM amino acid substitutions (AASs) and all SwissProt Variant (SwissVar) disease-related AASs to reference sequences and confidently mapped 99.96% of all AASs to the genomic loci. Based on the results, we developed an online database and interactive web server (M2SG) to (i) retrieve the mapped OMIM and SwissVar variants for a given protein sequence; and (ii) obtain related proteins and mutations for an input disease phenotype. This database will be useful for analyzing sequences, understanding the effect of mutations, identifying important genetic variations and designing experiments on a protein of interest.

AVAILABILITY AND IMPLEMENTATION:

The database and web server are freely available at http://prodata.swmed.edu/M2S/mut2seq.cgi.

PMID:
24002112
PMCID:
PMC3810852
DOI:
10.1093/bioinformatics/btt507
[Indexed for MEDLINE]
Free PMC Article

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