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This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

UASIS: Universal Automatic SNP Identification System

Danny C C Poo1*, Shaojiang Cai1 and James T L Mah2

Author affiliations

1 Department of Information Systems, School of Computing, National University of Singapore, 13 Computing Drive, Singapore 117417

2 Data Mining Department, l2R, A*STAR, 1 Fusionopolis Way #21-01 Connexis (South Tower), Singapore 138632

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Citation and License

BMC Genomics 2011, 12(Suppl 3):S9  doi:10.1186/1471-2164-12-S3-S9

Published: 30 November 2011

Abstract

Background

SNP (Single Nucleotide Polymorphism), the most common genetic variations between human beings, is believed to be a promising way towards personalized medicine. As more and more research on SNPs are being conducted, non-standard nomenclatures may generate potential problems. The most serious issue is that researchers cannot perform cross referencing among different SNP databases. This will result in more resources and time required to track SNPs. It could be detrimental to the entire academic community.

Results

UASIS (

    U
niversal
    A
utomated
    S
NP
    I
dentification
    S
ystem) is a web-based server for SNP nomenclature standardization and translation at DNA level. Three utilities are available. They are UASIS Aligner, Universal SNP Name Generator and SNP Name Mapper. UASIS maps SNPs from different databases, including dbSNP, GWAS, HapMap and JSNP etc., into an uniform view efficiently using a proposed universal nomenclature and state-of-art alignment algorithms. UASIS is freely available at http://www.uasis.tk webcite with no requirement of log-in.

Conclusions

UASIS is a helpful platform for SNP cross referencing and tracking. By providing an informative, unique and unambiguous nomenclature, which utilizes unique position of a SNP, we aim to resolve the ambiguity of SNP nomenclatures currently practised. Our universal nomenclature is a good complement to mainstream SNP notations such as rs# and HGVS guidelines. UASIS acts as a bridge to connect heterogeneous representations of SNPs.