title: Tools, resources and databases for SNPs and indels in sequences: a review.
abstract: Single Nucleotide Polymorphism (SNP) is a mutation where, a single base in the DNA differs from the usual base at that position. SNPs are the marker of choice in genetic analysis and also useful in locating genes associated with diseases. SNPs are important and frequently occurring point mutations in genomes and have many practical implications. In silico methods are easy to study the SNPs that are occurring in known genomes or sequences of a species of interest during the post genomic era. There are many on-line and stand alone tools to analyse the SNPs. We intend to guide the reader with the software details such as algorithmic background, file requirements, operating system specificity and species specificity, if any, for the tools of SNPs detection in plants and animals. We also list many databases and resources available today to describe SNPs in wide range of organisms.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, USA.
authors.forename: Abhik
authors.initials: A
authors.lastname: Seal
authors.affiliation: School of Computer Science and Information Technology, Devi Ahilya Vishwavidyalaya (DAVV), Indore 452 013, India; Computational Biology Group, Abhyudaya Technologies, Indore 452 003, India.
authors.forename: Arun
authors.initials: A
authors.lastname: Gupta
authors.affiliation: Department of Biotechnology and Bioinformatics, Kuvempu University, Jnaneshwari, Shankaraghatta 577 451, India.
authors.forename: M
authors.initials: M
authors.lastname: Mahalaxmi
authors.affiliation: Cannanore Cantonment Board, Kannur 670 017, Kerala, India.
authors.forename: Riju
authors.initials: R
authors.lastname: Aykkal
authors.affiliation: Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology (JUIT), Waknaghat, Solan 173 234, India.
authors.forename: Tiratha Raj
authors.initials: TR
authors.lastname: Singh
authors.affiliation: ICAR Research Complex for Goa, Ela, Old Goa 403 402, India.
authors.forename: Vadivel
authors.initials: V
authors.lastname: Arunachalam
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D057225:Data Mining / Q000379:methods; D030541:Databases, Genetic; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA
keywords: SNP detection; SNPs; bioinformatics; data mining; databases; expressed sequence tags; indels; molecular markers; point mutations; sequences; single nucleotide polymorphisms; software