Gene Knockout Mice

The Gene Expression Programming Framework in Java.It separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes in the chromosome. Platforms: Windows, Mac, Linux

EPTable is a simple web-based tool to analyze microarray gene expression profiles with additional gene profiles. Platforms: Mac, BSD, Linux

Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity. Platforms: Windows, Mac, Linux

EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries and provides several layers of annotation based on Entrez Gene to allow the user to highlight useful genes and manage cDNA library projects. Platforms: Windows, Mac, 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

IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info Platforms: Windows, Mac, Solaris, Linux

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms). Platforms: Windows, Mac, Linux

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments. Platforms: Windows, Mac, Linux

Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes. Platforms: Windows, Mac, Linux

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE) Platforms: Windows, Mac, Linux

The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites. Platforms: Mac, BSD, Linux

RmiR is an R package for the analysis of microRNA and gene expression microarrays.The package is designed to coupling microRNA and gene expression data, using different databases, like TargetScan, mirBase, picTar,TarBase and others... Platforms: Windows, Mac, Linux

RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment). Platforms: Windows, Mac, Linux

SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments. Platforms: *nix

In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed... Platforms: Matlab

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix... Platforms: Matlab

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

General implementation of matlab version of Viterbi algorithm specifically written for gene structure finding problem in mind. However, it can be modified to suit the goal of a user.Input:Transition Probability MatrixEmission Probability MatrixInitial Probability MatrixStates Matrix (ie.... Platforms: Matlab

Recent studies describe that the level of gene expression between species is positively correlated with the time that has passed since the species split from a common ancestor (Ranz et al., 2006). Moreover, Khaitovich et al. (2004) found a linear relationship between divergence time and... Platforms: Mac

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac