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AbiWord is a free word processing program similar to Microsoft® Word.
AceDB is a genome database designed specifically for handling bioinformatic data flexibly. It includes tools designed to manipulate genomic data, but is increasingly also used for non-biological data.
Free software for viewing and printing Portable Document Files
Alscript is a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow compex effects.
AlternaTIFF is a web browser add-on (ActiveX control or plug-in) that displays most of the common types of TIFF files. It works in most web browsers for Windows 95 or higher (98, ME, NT4, 2000, XP).
The American Type Culture Collection is a global nonprofit bioresource center that provides biological products, technical services, and educational programs to private industry, government, and academic organizations around the world.
Tools for high performance computing
Providing information for improved animal care and use in research, teaching, and testing.
This page attempts to summarise useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies and crystal structures and links to other antibody-related information.
The Ohio State University Arabidopsis Gene Regulatory Information Server is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes.
The Arabidopsis Information Resource provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant.
Argus is a microarray database software system designed to process, analyze, manage, and publish microarray data. Welcome to the Argus license and download page. If you are from a non-profit institution, you can freely download and use Argus.
ArrayExpress is a public repository for microarray data, which is aimed at storing well annotated data in accordance with Microarray Gene Expression Data Society recommendations.
Resources for Molecular and Cell Biologists
A Respository for Data from NMR Spectroscopy on Proteins, Peptides and Nucleic Acids.
Servers, Software & Databases.
The BioNetbook is a directory of Web pages for Biology.
BioProtocol assembled an extensive collection of high quality life science protocols.
Biology in silico
Biochemical Databases at The University of Cambridge.
Biochemical Web Servers at The University of Cambridge.
Biochemie.net is the first-line, catalogue oriented portal for the biosciences.
lots of programs
Bioinformatics.Org is an international organization which promotes freedom and openness in the field of bioinformatics.
Tools for bioinformatic
Tools to Discover
Information in the life sciences.
Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Biomolecular Interaction Network Database (BIND) is an expanding database of biomolecular interaction, pathway and complex information. All information is stored in BIND records that are freely available through a web interface that allows users to query, view, and submit records.
By scientists. For scientists.
Human and Mouse gene expression database
Bookends 8 is the reference manager that Mac users have been waiting for: Unicode-savvy, powerful group-based navigation, built-in HTTP server, Internet library searches, automated PubMed searches, and much more.
Web-based Buffer Calculations
Cytokines Online Pathfinder Encyclopaedia
A 'module map' showing conditional activity of expression modules in cancer
chemical drawing and graphics software
Compound Analysis Software & Databases, Cheminformatics
Databases and other resources designed to help you search for information by chemical name or structure.
Molar Conversions, Periodic Table and Equation Balancer
CLUSTALX - Graphical multiple alignment
COMe is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif. A bioinorganic motif may be defined as a common structural feature of a class of functionally related, but not necessarily homologous, proteins, that includes the metal atom(s) and first coordination shell ligands.
Programs and World Wide Web servers useful in comparative modeling
The Concurrent Versions System is the dominant open-source network-transparent version control system.
Identification of consensus patterns in unaligned DNA and protein sequences
DAN Data Bank of Japan is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters.
The DNA Concentration Calculator
The DNA ligation calculator
The Dali server is a network service for comparing protein structures in 3D.
Human 2-D-PAGE Databases for proteome analysis in health and disease
The Database of Interacting Proteins database catalogs experimentally determined interactions between proteins.
The primary goal of DOT is obtain a short list of candidate positions in a relatively short time. A "position" in this context refers to a relative orientation between a pair of molecules, defined in terms of a rotation and translation of three-dimensional space.
Database for Annotation, Visualization and Integrated Dicovery
From the Biomolecule to the Biosphere
Desktop Image Processing
Developmental Studies Hybridoma Bank at the University of Iowa
Dino 3D
This and two continuing pages include descriptions, references, and links to download pages for our laboratory software, all of which is free and open-source.
Evolutionary Lineage Inferred from Structural Alignment
The European Molecular Biology Open Software Suite (EMBOSS) is a package of high-quality free Open Source software for sequence analysis.
Ensembl presents up-to-date sequence data and the best possible automatic annotation for eukaryotic genomes.
EBI Databases
Expert Protein Analysis System Molecular Biology Server
Expression Profiler is a set of tools for clustering, analysis and visualization of gene expression and other genomic data.
The Fish Base
The Flavornet contains a compilations of aroma compounds sorted by their chromatographic and sensory properties.
The WWW Virtual Library: Drosophila melanogaster
The Fly Base
An Online Atlas and Database of the Drosophila Nervous System.
Fly Enhancer is a search engine designed to find clusters of binding sites (or any sequences of nucleotides) in the Drosophila melanogaster genome.
Drosophila melanogaster genetic resource at the National Institute of Genetics, Japan
The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center.
A comprehensive protein interaction map for Drosophila melanogaster
A cyberspace guide to Drosophila genes and their roles in development.
FlyMove is an internet resource to study the development of the fruit fly Drosophila melanogaster, aimed at university students and teachers of developmental biology classes. It will provide you with a variety of images, movies and interactive Shockwaves, which will facilitate the understanding of complex developmental processes.
A database of Drosophila nomenclature
This is the public gateway to the ongoing P-element Screen / Gene Disruption Project of the Bellen/Rubin/Spradling labs.
The EP lines allow GAL4-mediated overexpression of genes adjacent to the EP transposon and were generated by Pernille Rorth while at the Carnegie Institution of Washington (Proc. Natl. Acad. Sci. USA. 1996. 93: 12418-12422). The EP lines are provided for not-for-profit research and educational uses only.
The Bloomington Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.
The Flytrap web site acts as a central data repository for Drosophila melanogaster transgenic lines being created using an intron protein trap strategy.
A Drosophila Image Database
The Free Software Directory is a project of the Free Software Foundation (FSF) and United Nations Education, Scientific and Cultural Organization (UNESCO). We catalog useful free software that runs under free operating systems ¿ particularly the GNU operating system and its GNU/Linux variants.
This page contains links to free software packages that you can download and install on your computer for stand-alone (offline, non-Internet) computing.
Functional Magnetic Resonance Imaging is a public respository of peer-reviewed Functional Magnetic Resonance Imaging studies and their underlying data.
Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.
The goal of the Gene Ontology Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.
The Gene Ontology Tree Machine is a web-based platform for interpreting microarray data or other interesting gene sets using Gene Ontology hierarchies and is free to academic users after registration.
Biological databases
GeneCards is a database of human genes, their products and their involvement in diseases.
A family of gene prediction programs provided by Mark Borodovsky's Bioinformatics Group at the Georgia Institute of Technology, Atlanta, Georgia.
The General Repository for Interaction Datasets
This is the home page of the Generic Model Organism Project, a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology.
Generic Model Organism Database Construction Set
Table of Standard Genetic Code
GenoList genome browser
The Genome Knowledgebase is a database of cellular level processes from "simple" events, such as biochemical reactions, to "complex" events, such as the cell cycle. The Genome Knowledgebase provides process-level annotation of the structure and function of the Human Genome, with dynamic links to other databases relevant to the human system, and to the relevant literature.
Human Genome Most Used Links
Lists of Genome Sites
GENOTEXT (GENOmics conTEXT) is an automated sytem that determines the experimental context of samples and data sets in the NCBI Gene Expression Omnibus. It extracts the contextual identifiers and annotations of samples and models these annotations using the largest available compendium of biomedical vocabularies, the Unified Medical Language System (UMLS).
Identification of complete gene structures in genomic DNA
The Gene Expression Omnibus is a high-throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval.
Graphical Representation and Analysis of Structural Properties is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
Free/Shareware Graphic Software
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Human gene database,
with Integrative Annotation Validated
by Full-Length cDNA Clones.
This resource contains extensive information about selected biological factors (proteins, genes, etc.).
The IARC TP53 database includes all TP53 gene mutations identified in human cancers and published in the peer-reviewed literature.
Information Hyperlinked over Proteins
The Illinois Researcher Information Service (IRIS) offers the IRIS Database of federal and private funding opportunities in all disciplines; the IRIS Alert Service; and the IRIS Expertise Service.
The Catalogue of Imprinted Genes and Parent-of-origin Effects in Humans and Animals currently contains over 300 entries.
This is an archive of biology data and software, established in 1989, to promote public access to freely available information, primarily in the field of molecular biology.
The Integrin Page
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
Analysis of the false positives
The Intronerator
iSPOT is a web tool developed for the prediction of protein-protein interaction mediated by families of peptide recognition modules, and based on the SPOT software.
Jarte is a powerful, free word processor from Carolina Road Software.
2500+ strains
Kinase.com is a protein kinase gene resource.
LabOnWeb.com is the first life science research engine, a collection of gene discovery tools designed to accelerate work in the lab, improve the quality and accuracy of experiments, simplify the delivery of information and help researchers make more informed decisions throughout the discovery process.
A Guide to Cell Biology on the Web
Regulated Protein Turnover Resource Site
The logos server of the Max Planck Institute for Molecular Genetics, Berlin, Germany, offers software and online tools for the generation of different varieties of Sequence and Hidden Markov Models Logos.
The Longhorn Array Database (LAD) povides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. LAD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, LAD provides interfaces for data retrieval, analysis, and visualization.
MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces.
Median Fluorescence Intensity Freeware
The MEME/MAST system allows you to
discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and
search sequence databases using motifs using MAST.
Minimum information about a microarray experiment
The Molecular Interactive Collaborative Environment is developing new methods of collaborative, interactive visualization of complex scientific data.
Microarray Comparison Visualization Tool is a set of programs together with a web-interface for comparing, exploring and visualizing correlated genes in two microarray experiments that survey a range of conditions.
Practical Molecular Biology
A comprehensive collection of molecular biology protocols, molecular biology methods, molecular biology techniques, molecular biology procedures, molecular biology strategies, general laboratory protocols, laboratory techniques, laboratory methods, and procedures.
Molecular Biology Protocols
Molecular Biology Shortcuts is fully dedicated to BioInformatics and services for molecular biology scientists.
Software for the Molecular Biologists
Table of Contents for Molecular Modeling and Simulation Applications (Center for Structural Biology, Yale University)
Molecular Visualization Freeware
two-dimensional molecule drawing program
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
Motif scanning means finding all known motifs that occur in a sequence. This form lets you paste a protein sequence, select the collections of motifs to scan for, and launch the search.
This project aims to be a quantitative and comprehensive atlas of gene expression in mouse development.
This is a digital Atlas of mouse embryonic development.
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
The National Cancer Institute Mouse Models of Human Cancers Consortium is a collaborative program designed to derive and characterize mouse models, and to generate resources, information, and innovative approaches to the application of mouse models in cancer research.
The p53 Mutation Database contains information on 4,360 mutations found in the human p53 gene gathered from 416 literatures.
NIH Image
Prediction of N-terminal acetylation sites
The NF-kB Signal Trasduction Pathway
The Nucleic Acid Calculator
Nucleic Acid Database assembles and distributes structural information about nucleic acids.
The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.
The Oligo Calculator
Welcome to Oncomine, a resource for examining gene expression in cancer. The goal of the project is to collect, standardize, analyze, and deliver published cancer gene expression data to the research community.
Open Source Software
The Open Directory Project is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors.
A free web browser.
The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain.
Osprey is a software platform for visualization of complex interaction networks.
Parallel Protein Information Analysis system
The Periodic Table on the web.
In 1986 Martin C. Rechsteiner and Scott W. Rogers proposed that polypeptide sequences enriched in Proline (P), glutamic acid (E), serine (S) and threonine (T) target proteins for rapid destruction. During the past years scientific research provide strong evidence that PEST regions do, in fact, serve as proteolytic signals.
The purpose of a Phosphoprotein Database is to promote a systematic approach to the study of cellular protein phosphorylation.
in-vivo phosphorylation sites in human and mouse proteins
PHYLIP is a free package of programs for inferring phylogenies.
Tools for phylogenetic footprinting purposes
Protein Information Resource
Software for plasmid construction and visualization
The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.
The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports.
PredictProtein is a service for sequence analysis, and structure predication.
NUCLEOTIDE SEQUENCES, AMINO ACID SEQUENCES
Primer Input
Ultimate PCR Primer Design Tools
ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases
Procheck checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
The program supports analysis of 2D, 3D, and 4D NMR spectra.
The Protein Calculator
The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
The human Tumor Necrosos Factor alpha / Nuclear Factor [kappa] B Protein Interaction Network
ProtoNet provides global classification of the proteins into hierarchical clusters.
your lab's reference book
A resource for protein chemistry and mass spectrometry.
The Life Sciences Search Engine
The Life Sciences Search Engine : Welcome to the new cross-database search page.
The RNA Resource
The RNA Probe Specific Activity Calculator
Free software for RNA secondary structure prediction, structure comparison and sequence design.
The RNA Structure Database offers access to a relational database containing data about all publicly available RNA structures using a web driven interface.
This web resource lists Internet links on RNA related topics.
An RNAi Design Tool
The goal of the RNAi Codex is to provide a single database that curates publicly available RNAi resources.
The 'Open Access RNAi Program' from Open Biosystems is aimed at enabling the life science community through straight-forward access to the latest technologies developed in the field.
Each entry in the miRNA Registry represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching using BLAST, and entries can also be retreived by name, keyword, references and annotation.
Although hundreds of miRNAs have been discovered in mammalian genomes, the function of less than a handful of miRNAs is known. This viewer allows access to the predicted protein coding gene targets that are conserved between human and mouse/rat. Searching by miRNA will display a ranked list of gene targets and allow you to analyze each conserved target gene/sites in detail.
The siRNA user guide
Dharmacon siDESIGN Center
Jack Lin's siRNA sequence finder
The RNase P Database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information.
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
Reactome is a knowledgebase of biological processes.
The Restriction Enzyme Database
The Reference Sequence collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
Welcome to RestrictionMapper - Now with Virtual Digest
Reverse Complement converts a DNA sequence into its reverse, complement, or reverse-complement counterpart.
Rose - random model of sequence evolution
Rotor Calculations
Science and Mathematics Resources
Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D.
Web Program Tools and Databases in Molecular Biology
Sequence Analysis Server for Analysis of DNA and Protein Sequences
Online sequence analysis tools
The Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in cell signaling.
Interactive graphic models of molecular and cellular pathways.
Simple Modular Architecture Research Tool (SMART)
Software for Protein-Protein Docking
Genomic Resources
Los Alamos National Laboratory Bioscience Division
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes
This document describes the necessary strains to construct and test fusions between the N-terminal DNA binding domain of lambda repressor and your favorite protein. These strains are freely available to anyone who wants to use this method. I only ask that people keep me informed if using the method does something useful.
RNA Secondary Structure Java Applet Freeware
Access methods and online resources of potential interest to scop users
The activities of BioSync include documenting the needs of structural biologists for synchrotron radiation, evaluating the status of existing and planned facilities, recommending funding and access policies, lobbying in Washington for improved support of synchrotron rings and beamlines, and organizing a web-based clearinghouse of beamline information.
Tools for data mining provided by The National Center for Biotechnology Information, The U.S. National Library of Medicine and The National Institutes of Health
This web site describes the systems, gives references and abstracts of publications, is a repository of experimental results and a forum for researchers.
The Transport Protein Database
The Tumor Gene Family of Databases contains information about genes which are targets for cancer-causing mutations; proto-oncogenes and tumor supressor genes.
Software and Resources for Macromolecular Crystallography and Structural Biology
The Vector Database contains annotations and sequence information for many vectors commonly used in molecular biology.
All the Virology on the WWW seeks to be the best single site for Virology information on the Internet.
The Visualization and Analysis Tool for Biological Interaction Data (VisANT) is an application for integrating biomolecular interaction data into a cohesive, graphical interface. VisANT is free to academic community and is an open-source project.
Protein sequences, references, functional data and many other relevant data are included in this database.
Web Antibody Modelling
DNA and Purpose Entry
Webcutter is a free on-line tool to help restriction map nucleotide sequences.
Whitehead Institute Center for Genome Research Scientific Resources allows researchers to gain around-the-clock access to WICGR software, protocols, data, and publications.
A database on Wnt genes.
Caenorhabditis elegans WWW Server
a database of behavioral and structural anatomy of Caenorhabditis elegans
The Wormbase
Information pertaining to the cell and developmental biology of the frog, Xenopus.
Full public access to the data and reagents generated from ongoing functional analysis of the yeast genome.
The yeast cell cycle analysis project's goal is to identify all genes whose mRNA levels are regulated by the cell cycle.
The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast Saccharomyces cerevisiae.
Yeast Transformation Information
The Zebrafish Information Network serves as the zebrafish model organism database.
The Zebrafish Information Server
The open-access register for zoological taxonomy
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