Fqutils provides a basic set of bioinformatics command line tools for working with sequence data in FASTQ format. It complements Greg Hannon's fine Fastx Toolkit suite. One characteristic of Fqutils is that it correctly handles the full FASTQ format as described by the published standard, which specifically allows multi-line sequence and quality score information per record. Fqutils is intended to be useful as part of the early portions of post-sequencing pipelines and quality assessment processes.
FreeMED is a Web-based medical records (EMR) and patient management system with a printing system, patient scheduling, an HL7 interface, a billing system, XML-RPC Web services, and many other features. It has an extensible modular architecture, allowing it to be customized based on individual practices without having to rewrite core components of the system. It is HIPAA compliant.
GENtle is bioinformatics software for everyday molecular biology tasks. It features DNA and amino acid sequence display and editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, primer design, virtual PCR, online database access, graph/spectra display, PHYLIP interface, and more.
GRIDportal is a Web-based application portal that acts as a frontend to GRID computing. Its aim is to make common GRID applications like Abaqus, Matlab, or BLAST more accessible to the user. Use of GRIDportal does not require any knowledge of Unix nor GRID computing whatsoever. All the user needs to know is how to use the given application, so the step from desktop computing to GRID computing should thus become a much smaller one than it otherwise would be.
GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
GeneX Va is a gene expression database supporting storage and analysis of Affymetrix GeneChip technology. It is designed to serve as a secure repository and archive for many researchers' data. It is typically expected to be installed as part of a microarray center; the software is compact enough to install for a single department or even a single user. It includes an Analysis Tree package which includes an ever-expanding set of analytical tools, and has plug-in architecture allowing easy expansion. The "Va" in the name stands for the University of Virginia version, which is a total rewrite of what was originally NCGR's GeneX.
GenomePixelizer 2D plotter (or genoPix2D) generates images (actually interactive canvases) of genomic similarity dot plots in which each "dot" indicates similarity between a pair of genes. Diagonal runs of dots generally indicate collinearity (or synteny) in the genomic regions being compared. The program can compare large (chromosome-scale or even eukaryotic genome-scale) genomic regions, and can produce PostScript output of the dot plots. Images on a genoPix2D canvas are not static. They are interactive, and every dot (element) is associated with corresponding gene annotations that are searchable by gene ID or keyword.
Genomorama is a software program for interactively displaying multiple genomes. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit). Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC), and Linux (using Motif). Executables and source code are freely provided for all flavors.