Genes

Evocosm is a C++ Framework for Evolutionary Computing library. Evocosm is a set of classes that abstract the fundamental components of an evolutionary algorithm. Ill list the components here with a bit of introduction; you can review the details of the classes by downloading the code archives... 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

Peptide::Pubmed is a Perl module that can extract peptide sequences from MEDLINE article abstracts. SYNOPSIS use Peptide::Pubmed; $parser = Peptide::Pubmed->new; $in = { PMID => q[15527327], Author => q[Doe JJ, Smith Q], Journal => q[J Biological Foo. 2004;8(2):123-30.], Title => q[Foo,... Platforms: *nix

Bio::GMOD is a unified API for Model Organism Databases. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $mod->live_version; Update a MOD installation use Bio::GMOD::Update;... Platforms: *nix

Take It! takes a screenshot of your current screen, puts it into a file, and uploads it to a webserver trought FTP. You can freely customize periods of time for your capture, and then see what its going on in your machine remotely. Platforms: Mac

Nowadays, the use of so-called RNA interference is a common technique applied by molecular biologists to determine the function of the many genes in our genome.Unfortunately, the design of oligonucleotides, the building blocks for this technique, is a time-consuming and error-prone task. iRNAi... Platforms: Mac

XPlasMap... Draw plasmid & genomic DNA maps showing restriction sites, genes, multiple cloning sites, and other features; copy and paste between maps; import from GenBank files; save as JPG or PNG Platforms: Mac

GProcessor is a small, easy to use application specially designed to help you with the statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis. Microarray is one of the most fascinating technologies in the millennium. It is a novel invention to exploit DNA... Platforms: Windows

FastSemSim is specially designed as a handy Python-based efficient implementation of a couple of semantic similarity measures. The main target of the project is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology Platforms: Windows

GenomePixelizer is a program for comparative genomics, detection of duplication events in genomes, tracking the 'footprints' of evolution. It may be considered as a drawing tool that generates custom images of genomes out of the given set of genes. Platforms: Windows, Mac, BSD, Linux

QTL Reaper analyzes data from progeny of a genetic cross in experimental plants or animals. It seeks the location of genes that affect a heritable trait, and it is specially designed for analysis of gene expression measurements. Platforms: Mac, Linux

Find restriction enzymes that help differ known homologe DNA sequences (RFLP). Simulate electrophoresis gels. Usefull to investigate the diversity of a population by one of their common genes. Written in perl, uses bioperl modules and the GD library. Platforms: Windows, Mac, Linux

Syntainia is an innovative tool for visualization of multiple genomes. It presents a simple and intuitive user interface to view and manipulate relationships between groups of genes. With a clearer gene visualization, it is easier for the researcher to identify synteny conservation among multiple... Platforms: Mac

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types. Platforms: Windows, Mac, Linux

Learn the sounds of the Spanish Alphabet. Get ready to read Spanish! Aprendan los sonidos del alfabeto español. ¡Prepárense para leer en español! 4 phonetic matching phonetic photo images are matched with each letter to help your child learn the sound of each letter. 4 fonetica... Platforms: Mac

MCGH is a Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome. M-CGH allows us to visualize the copy number changes... Platforms: Matlab

Genes4all is a package of modules for visualizing bioinformatic information using GMOD, BioPerl and Chado. It depends on the gmod_dbsf module (http://drupal.org/project/gmod_dbsf) and is in active development. See also http://drupal.org/project/biosoftware_bench.Currently two (sub)modules are... Platforms: PHP

This projects simulates the evolution of critters in their environment. There are 32 critters which all have DNA in the form of two 8-bit numbers (actually they are 32-bit, but only 8 bits are used). The first set of genes determines the color of the critter. The other set of genes are sex genes.... Platforms: Mac

HaMSTR is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes. A-priori knowledge about orthology-relationships among genes in different sets of reference species is extracted from the Inparanoid-Database.... Platforms: Mac

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