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Database Commons - SNPLogic

SNPLogic

Citations: 26

z-index 0.81

Short name SNPLogic
Full name
Description SNPLogic brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects.
URL http://www.snplogic.org/
Year founded 2009
Last update & version 2009-01-01    v1.0
Availability Free to all users
University/Institution hosted University of California San Francisco
Address 1650 Owens Street,San Francisco, CA 94158, USA
City San Francisco
Province/State CA
Country/Region United States
Contact name Alexander R. Pico
Contact email apico@gladstone.ucsf.edu
Data type(s)
Major organism(s)
Keyword(s)
  • SNP
Publication(s)
  • SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. [PMID: 18984625]

    Alexander R Pico, Ivan V Smirnov, Jeffrey S Chang, Ru-Fang Yeh, Joseph L Wiemels, John K Wiencke, Tarik Tihan, Bruce R Conklin, Margaret Wrensch
    Nucleic acids research 2009:37(Database issue)
    26 Citations (Google Scholar as of 2016-01-27)

    Abstract: SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data.

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Tags

DNA
Homo sapiens
SNP

Record metadata

  • Created on: 2015-07-27
  • Curated by:
    • Lin Xia [2016-04-11]
    • Lin Xia [2016-03-28]
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