NDLI: FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

Content Provider	PubMed Central
Author	Yuan, Hsiang-yu Chiou, Jen-jie Tseng, Wen-hsien Liu, Chia-hung Liu, Chuan-kun Lin, Yi-jung Wang, Hui-hung Yao, Adam Chen, Yuan-tsong Hsu, Chun-nan
Copyright Year	2006
Abstract	Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by simply deploying more Web wrapper agents. To validate the results of our prioritization, we analyzed 1569 SNPs from the SNP500Cancer database. The results show that SNPs with a high predicted risk exhibit low allele frequencies for the minor alleles, consistent with a well-known finding that a strong selective pressure exists for functional polymorphisms. We have been using FASTSNP for 2 years and FASTSNP enables us to discover a novel promoter polymorphism. FASTSNP is available at .
Related Links	http://dx.doi.org/10.1093/nar/gkl236
Starting Page	635
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Web Server issue
Volume Number	34
Language	English
Publisher	Oxford University Press
Publisher Date	2006-07-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

Congenital scoliosis: an up-to-date

Pneumothorax: an up to date “introduction”

iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

A Meta-Analysis Strategy for Gene Prioritization Using Gene Expression, SNP Genotype, and eQTL Data

SNP prioritization using a Bayesian probability of association

Biomarkers in Multiple Sclerosis: An Up-to-Date Overview

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

Similar Documents

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

BacMap: an up-to-date electronic atlas of annotated bacterial genomes

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

Congenital scoliosis: an up-to-date

Pneumothorax: an up to date “introduction”

iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

A Meta-Analysis Strategy for Gene Prioritization Using Gene Expression, SNP Genotype, and eQTL Data

SNP prioritization using a Bayesian probability of association

Biomarkers in Multiple Sclerosis: An Up-to-Date Overview

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization