RESUMO
BACKGROUND: With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating. RESULTS: FANS http://fans.ngc.sinica.edu.tw/ harnesses the power of public information databases and powerful tools from six well established websites to enhance the efficiency of analysis of novel variations. FANS can process any point change in any coding region or GT-AG splice site to provide a clear picture of the disease risk of a prioritized variation by classifying splicing and functional alterations into one of nine risk subtypes with five risk levels. CONCLUSION: FANS significantly simplifies the analysis operations to a four-step procedure while still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize the variations and select the ones with most functional impact for validation. Additionally, the program offers a distinct improvement in efficiency over manual operations in our benchmark test.
Assuntos
Biologia Computacional/métodos , Mutação , Polimorfismo de Nucleotídeo Único , Animais , Automação , Variação Genética , Genoma , Genoma Humano , Genômica , Humanos , Camundongos , Linguagens de Programação , Risco , Análise de Sequência de DNA/métodos , SoftwareRESUMO
A human gene association study often involves several genomic markers such as single nucleotide polymorphisms (SNPs) or short tandem repeat polymorphisms, and many statistically significant markers may be identified during the study. GenoWatch can efficiently extract up-to-date information about multiple markers and their associated genes in batch mode from many relevant biological databases in real-time. The comprehensive gene information retrieved includes gene ontology, function, pathway, disease, related articles in PubMed and so on. Subsequent SNP functional impact analysis and primer design of a target gene for re-sequencing can also be done in a few clicks. The presentation of results has been carefully designed to be as intuitive as possible to all users. The GenoWatch is available at the website http://genepipe.ngc.sinica.edu.tw/genowatch.
