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.

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…Population genomics examines the genetic variation within and between populations that is scattered across the entire genome to assess the demographic history, phylogenetic relations and selective pressures of a species (Jorde, 2001). Several types of genomic data can be evaluated at the population level, including single nucleotide polymorphisms (SNPs), indels and copy number variations; but SNPs are the most commonly analyzed of the three (Seal et al, 2014). All population-level sequencing techniques share common pitfalls that should be known and avoided before investing any money on sequencing.…”

Advances in the genome-wide association study of chronic hepatitis B susceptibility in Asian population

“…SNP is the most common genetic variation in human, accounting for over 90% of all known polymorphisms. In recent years, as the third generation of genetic markers, SNP has been widely used to search for disease-related genes and to explain the difference among individuals and groups in terms of the susceptibility to the disease and the disease progression [ 11 ]. Traditional analysis of the association between complex diseases and candidate genes usually selects one or a few disease-related candidate genes based on an understanding of the disease; therefore, genes and SNP loci for study are poorly available.…”

High mobility group box 1 protein polymorphism affects susceptibility to recurrent pregnancy loss by up-regulating gene expression in chorionic villi

“…Single-nucleotide polymorphisms (SNPs) may affect the development of human diseases by interfering with gene expression [12]. In the current study, we first investigated the association between HMGB1 genetic polymorphisms and susceptibility to RPL.…”