SIMP (SNP Information Mining Pipeline) -- Tools for SNPs data collection, integration, selection and preparation for association study on complex diseases. It serves both candidate gene-based approach and positional cloning-based approach.
Human data (Genome, Gene, and SNP) only!
For the time being, in short of support, dbSNP data is not completed updated. So, you should be able to get more data from dbSNP than from here. For this reason, all SNP-related data query might not be complete, including rs ID query, position-based query, and flanking sequence query. Be cautious using this data.
Expecting a major update in the Summer.
Some tools will work for studies of the other species, if you do not need to use data provided by our systems, including genome sequence, SNPs, etc.
Existing
web sites for gene/SNP query
SNP data
collector
SNPQuery
SNPQuery-rslist: Search for SNP according to SNP rs IDs.
SNPQuery-Positioin: Search for SNP according to genomic position ranges.
SNPQuery-Genotype Data Batch Query: Search for HapMap and Perlegen SNP genotype data
Function SNP from dbSNP: Search for functional SNPs (coding and splicing) from dbSNP
FlankingSNPQuery: Search for SNPs mapped to adjacent locations of SNPs in the query list.
DNannotator can be used to map your own SNPs, which were discovered by local re-sequencing project, into any genomic DNA sequence, including the public assembly.
{Format4SNPBrowser is a tool to reformat DNannotator feature table into input format of SNPBrowser. The output of Format4SNPBrowser can be import as SNP list into SNPBrowser, so they can displayed with SNPs provided by Celera.}
Frequency Finder is a tool to search for SNP allele frequency data in batch mode.
SNPSequer is a tool to fetch flanking sequences with sufficient length for SNPs in batch mode
LD or haplotype analysis, though these tools are primarily designed to process data from HapMap, user's own formatted data can be analyzed too.
- HapMap-Haploview-Processor takes outputs from HapMap/Perlegen and Haploview, to create lists of tSNPs, SNPs within haplotype blocks, SNPs outside of blocks, and regions defined by SNPs. Gabriel's method, Four Gamete Rule, and Solid Spine of LD methods can be used in Haploview.
HapMap-LDSelect-Processor takes outputs from HapMap/Perlegen or user's own genotype and marker data, perform "LD Select" (Carlson et al. 2004) calculation. Creates lists of tSNPs, SNPs within haplotype blocks, and regions defined by SNPs.
SNP
Evaluator/Filter/Selector
SNP Evaluation/Selector (coming soon!)
SNP Filter
SNPFilter scores SNPs by function effect, and filters them by physical position, polymorphism type. Also mask out "excluded regions" - user can define regions to be excluded for consideration.
SNP Selector
SNPSelector picks SNPs based on output from SNPFilter, according to desired marker density and score.
SNP
Assay Designer
SNP Cutter is a tool to design (in batch mode) primers and select Restriction Enzymes for using PCR-RFLP to type SNPs
Primer Nerd is one simple tool to design batch primers needed to perform Fluorescence Polarization (FP) or other single-base extension based SNP genotyping.
PyroPrimer is a tool to design both PCR and sequencing primers for batch of SNPs for pyrosequencing assay. (Restricted to users at Dept of Psychiatry, U of C.)
Map primers to gDNA
plotPrimer maps Primers back to original gDNA sequence which was used for primer design, so that primer-primer relationship can be better viewed. Especially good for mutation screening primer evaluation.
- DNannotator maps primers to UCSC assembly chromosomes or any other gDNA sequences.
- SNPrimer maps Primers to (batch) SNPs' amplicons/gDNA sequence, for SNP genotyping primer evaluation (Pyrosequencing assay development)
Coming components:
Note: Several other functions are currently standalone functions. Implementation of web-based application is undergoing.
Please cite the references:
Chunyu Liu, Tu Nguyen, Ruifang Zhang, Fengxia Yao, Zanhua Zhu, Elliot S. Gershon. SNP Information Mining Pipeline (SIMP) for Complex Disease Studies. 53rd Annual Meeting of the American Society of Human Genetics. Los Angeles, CA, 4-8, November. Am J Human Genet 73(5):421. abstract# 1470.
Chunyu Liu, Tom I. Bonner, Tu Nguyen, Jennifer L. Lyons, Susan L. Christian, Elliot S. Gershon. DNannotator: annotation software tool kit for regional genomic sequences. Nucleic Acids Res. 2003. 31(13):3729-3735
Tu Nguyen, Chunyu Liu, Elliot S. Gershon, Francis J. McMahon. Frequency Finder: A multi-source web application for collection of public allele frequencies of SNP markers. Bioinformatics. 2004. 20(3):439–443
8/16/2004 updated
