Snp Genotyping

The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis Platforms: Windows, Mac, Linux

AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan® and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design... Platforms: Mac

Device::SNP is a Perl extension for the GE Fanuc SNP-X serial protocol as used by GE Fanuc DataPanel data terminals. See http://www.gefanuc.com/en/ProductServices/VisPCSolutions/DataPanel/index.html SYNOPSIS use Device::SNP; my $s = new Device::SNP::Slave( Portname => /dev/ttyUSB0, Debug... Platforms: *nix

SNP Analyser was developed as an easy-to-use and useful utility for the efficient analysis and management of Affymetrix SNP DMET Data analysis. SNP Analyser is a software that was designed with the help of the Java programming language. Platforms: Windows

This script reports various SNP density statistics across all markers in a marker mapped spreadsheet. Platforms: Mac

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data. Platforms: *nix

CNVision is a small, simple application designed to simplify CNV analysis of Illumina genotyping data. It will simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for... Platforms: Windows

bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow... Platforms: Windows, Mac, BSD, Linux

Returns the contingency tables for several markers in case control study.Simple count of SNP count according to the type of polymorphism. Platforms: Matlab

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation. PrimerPlex designs primers for multiplex PCR assays and... Platforms: Mac

Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago,... Platforms: Mac

AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data. Platforms: Mac, BSD, Linux

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies. Platforms: Windows, Mac, Linux

MAGMA: Multiobjective Analyzer for Genetic Marker AcquisitionA genetic algorithm for generating SNP tiling paths from a large SNP databasebased on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks):Hubley R., Zitzler Platforms: Windows, Mac, Linux

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly. Platforms: Mac

SnipPeep is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. Platforms: Mac

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description... Platforms: Matlab

This script creates a binary spreadsheet to indicate if there exists a rare variant in the window centered about the current marker. At chromosome edges, the maximum number of markers up to the window size is used without running into the next chromosome. Platforms: Mac

Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. For information on accessing B Allele Frequencies for Illumina data, Platforms: Mac

The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, such methods are suboptimal for a rapidly growing dataset, because they require significant... Platforms: Mac