Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: rNA: a fast and accurate short reads numerical aligner. Newsbot! Literature Watch 0 08-28-2012 02:00 AM
RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis. Newsbot! Literature Watch 6 02-06-2012 04:55 AM
PubMed: DECOD: fast and accurate discriminative DNA motif finding. Newsbot! Literature Watch 0 01-11-2012 10:40 AM
Introducing DARIO, a web service for the analysis of small RNA-seq data mfasold RNA Sequencing 0 06-27-2011 01:49 AM
GenomeQuest offers easy-to-use ChIP-Seq workflow as web cloud service GenomeQuest Vendor Forum 0 11-12-2009 07:41 AM

Thread Tools
Old 12-13-2012, 11:40 PM   #1
RSS Posting Maniac

Join Date: Feb 2008
Posts: 1,443
Default PubMed: VARIANT: Command Line, Web service and Web interface for fast and accurate fu

Syndicated from PubMed RSS Feeds

Related Articles VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8

Authors: Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J

The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at:

PMID: 22693211 [PubMed - indexed for MEDLINE]

Newsbot! is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:50 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO