Ten Bioinformatics Tools for Single Nucleotide Polymorphisms Detection

Single Nucleotide Polymorphisms (SNPs) as unique genetic variations are widely used as biomarkers for drug designing and development for individualized therapy. SNP genotyping techniques such as SBE with MS detection, SBE with fluorescence intensity detection, The FP-TDI, Pyrosequencing and The TaqMan 5’ nuclease assay are low-speed, time consuming and very expensive. To overcome such disadvantages, bioinformatics tools are emerged as alternative methods for detection of SNPs in different populations for different diseases such as cancer, diabetes, heart diseases, Down syndrome and other genetic related disorders to help in rapid and low-cost and high accuracy detection methods. In this review we have listed 10 bioinformatics tools for SNP detection to introduce them for the researchers who are interested in SNP detection required studies in order to help them in saving time and cost and enhancement of accuracy of their results. The bioinformatics tools are selected in this review are poly phred, HGBASE, Human chromosome 21 cSNP database, Dog Genome SNP Database, JSNP database, Polybays, novoSNP, HaploSNPer, PupaSNP and QualitySNPng, which have their own specific performance for detection of SNPs. Researcher can choice appropriate programs on the basis of their research’s need and application. We hope this review can be helpful and integrates scientific information with bioinformatics tools in drug discovery processes and other studies involved SNP detection and lead to short time-low cost and high accuracy biomarker detection in drug designing and development process.

[1]  Human genetic bi-allelic sequences (HGBASE), a database of intra-genic polymorphisms. , 1998, Memorias do Instituto Oswaldo Cruz.

[2]  C. van Broeckhoven,et al.  novoSNP, a novel computational tool for sequence variation discovery. , 2005, Genome research.

[3]  P. Sullivan,et al.  Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput , 2003, The Pharmacogenomics Journal.

[4]  Martijn van Kaauwen,et al.  QualitySNPng: a user-friendly SNP detection and visualization tool , 2013, Nucleic Acids Res..

[5]  Yusuke Nakamura,et al.  JSNP: a database of common gene variations in the Japanese population , 2002, Nucleic Acids Res..

[6]  Joaquín Dopazo,et al.  PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level , 2004, Nucleic Acids Res..

[7]  A. Rai,et al.  Biomarkers in the era of personalized medicine – a multiplexed SNP assay using capillary electrophoresis for assessing drug metabolism capacity , 2010, Scandinavian journal of clinical and laboratory investigation. Supplementum.

[8]  Lu Wang,et al.  DoGSD: the dog and wolf genome SNP database , 2014, Nucleic Acids Res..

[9]  Erica G. Jewell,et al.  Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers. , 2007, Methods in molecular biology.

[10]  Gabor T. Marth,et al.  A general approach to single-nucleotide polymorphism discovery , 1999, Nature Genetics.

[11]  Ben Vosman,et al.  HaploSNPer: a web-based allele and SNP detection tool , 2008, BMC Genetics.

[12]  P. Bucher,et al.  A cSNP map and database for human chromosome 21. , 2001, Genome research.

[13]  S. Fucharoen,et al.  Genetic polymorphisms and implications for human diseases. , 2007, Journal of the Medical Association of Thailand = Chotmaihet thangphaet.

[14]  C. P. Morris,et al.  SNP technologies for drug discovery: a current review. , 2008, Current drug discovery technologies.

[15]  M. Cargill.  Characterization of single-nucleotide polymorphisms in coding regions of human genes , 1999, Nature Genetics.

[16]  R B Altman,et al.  The Pharmacogenetics Research Network: From SNP Discovery to Clinical Drug Response , 2007, Clinical pharmacology and therapeutics.

[17]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.