Gene Similarity

This script uses the gene name field(s) in a table downloaded from the UCSC Genome Browser to add gene names to an existing SVS marker map saved in the DSM file format. Note: Though the following instructions specify downloading a table containing genes based on the Mar. 2006 (NCBI36/hg18) Human... Platforms: Mac

Build a gene network! The lac operon is a set of genes which are responsible for the metabolism of lactose in some bacterial cells. Explore the effects of mutations within the lac operon by adding or removing genes from the DNA. Sample Learning Goals: * Predict the effects on lactose... Platforms: Mac

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)... Platforms: *nix

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #... Platforms: *nix

MeV or Multiple Experiment Viewer is a Java tool to help you with microarray gene expression data analysis. MeV supports 5 input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery. Platforms: Windows

MeV or Multiple Experiment Viewer is a Java tool to help you with microarray gene expression data analysis. MeV supports 5 input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery. Platforms: Mac

Wormbase Converter is a simple, easy to use application designed to help you with the conversion of any Gene ID into any other Gene ID. You can convert a "WormBase ID", a "Gene/Transcript/CDS Sequence Name" or a "Gene Name" into a "WormBase ID", a "Gene Sequence Name" or a "Gene Name". Moreover,... Platforms: Windows

BCLUST is a small, simple, command prompt based tool specially designed to help you asses reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method. Because of the rapid development of microarray technologies, many of statistical procedures, most... Platforms: Windows

siliColony is a small, simple, easy to use application specially designed to offer you a tool to help you estimate the probability that a modifier gene is responsible for the segregation of phenotypes. for WindowsAll Platforms: Windows

LDMgen is a small, easy to use, command prompt based application specially designed to offer users a tool to help you map the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies. The application comes with a default parameters file.... Platforms: Windows

SpliceGrapher predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments. FEATURES: · splice graph prediction ·... Platforms: Windows

The application loads microarray data (gene expression ratios) and determines which genes are up- or downregulated by a user-defined ratio cut-off level. For each experiment, lists of differentially expressed genes are computed. Every list will be compared to every other list, and the number of... Platforms: Windows

GMDR was built as an Open-Source interaction analysis instrument that is aimed to perform gene-gene interaction with generalized multifactor dimensionality methods. This Java-based tool offers a generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions. Platforms: Windows, 2K, XP, Windows Vista, 7

SimPack is specially developed for the research of similarity between concepts in ontologies or ontologies as a whole. Possible other application areas of SimPack include · the investigation of similarity between software source code. For instance to detect changes between classes of... Platforms: Windows

OrientationChecker is a simple, Java based application specially designed to help you check and alter the orientation of 16S rRNA gene sequences. Platforms: Windows

In signal processing, cross-correlation is a measure of similarity of two waveforms as a function of a time-lag applied to one of them. This is also known as a sliding dot product or inner-product. It is commonly used to search a long duration signal for a shorter, known feature. It also has... Platforms: Matlab

Sound-Similar (Free Version) is a lightweight software application that measures the perceptual similarity between two WAV files in Linear PCM format, the most commonly used format in WAV files. The degree of similarity is represented by a similarity score in percentage, from 0% to 100%. The... Platforms: Windows, Windows 7

Games::Battleship::Player is a Battleship player class. SYNOPSIS use Games::Battleship::Player; $aeryk = Games::Battleship::Player->new(name => Aeryk); $gene = Games::Battleship::Player->new(name => Gene); print Player 1: , $aeryk->name, "n", Player 2: , $gene->name, "n";... Platforms: *nix

Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1... Platforms: *nix

Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers... Platforms: *nix