SequenceVariantAnalyzer
   HOME

TheInfoList



OR:

SequenceVariantAnalyzer (SVA) is a computer program for annotating and analyzing
genetic variant Genetic variant may refer to: * Single-nucleotide polymorphism (SNP), in a case it is a common genetic variant * Mutation, in a case where it is a rare genetic variant * Copy-number variation * Variant (biology) See also * Genetic variation (disam ...
s called (identified) from a whole genome or
exome The exome is composed of all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing. This includes untranslated regions of messenger RNA (mRNA), and coding re ...
sequencing study (
Shotgun sequencing In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The Sanger sequencing#Method, chain-termination method of DNA sequencin ...
).


Introduction


Background

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of
linkage disequilibrium Linkage disequilibrium, often abbreviated to LD, is a term in population genetics referring to the association of genes, usually linked genes, in a population. It has become an important tool in medical genetics and other fields In defining LD, it ...
,{{cite journal, vauthors=Need AC, Goldstein DB, title=Next generation disparities in human genomics: concerns and remedies., journal=Trends in Genetics, year=2009, volume=25, pages=489–494, doi=10.1016/j.tig.2009.09.012, pmid=19836853 thus, in theory, is more possible to directly identify the genetic variants contributing to biological traits or medical outcomes. The rapidly evolving high-throughput DNA sequencing technologies have now allowed the rapid generation of large amounts of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is software that analyzes genetic variants identified in such studies.


Functions

SVA is designed for two specific aims: (1) To annotate the biological functions of the identified genetic variants and group them, conveniently; (2) To find the genetic variants that are associated with or responsible for the biological traits or medical outcomes of interest.


Language

SVA is developed on the
Java platform Java is a set of computer software and specifications that provides a software platform for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms fr ...
.


Authors

SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.


References


External links


SVA project website
Genetics software