Sites with Multiple or Integrated Tools
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Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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A. C. R. Martin Bioinfo Site
Downloadable Java software for bioinformatics, including a Needleman-Wunsch program and a protein structural least-squares fit program.
[Univ. of Michigan] (Naohiro Inohara) Analyzes DNA and protein sequences.
Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.
BCM Gene Finder
[Baylor College of Medicine] This service provides several tools that use the identification of certain regions (splice sites, protein coding exons, promotor and poly-A regions) in nucleic acid sequences to find possible genes.
BCM Search Launcher
[Human Genome Center, Baylor College of Medicine] A collection of molecular biology-related search and analysis services available on the WWW. Currently connects to a general protein sequence, or protein pattern searches, species-specific protein sequence searches, nucleic acid sequence searches, multiple sequence alignments, pairwise sequence alignments, gene feature searches, sequence utilities, and protein secondary structure prediction.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
Bioinformatics and Biological Computing
[Weizmann Institute of Science] This is home for a wealth of tools, databases, and information in bioinformatics. There are servers in the areas of sequence analysis, proteomics, and genomics, as well as downloads and educational products. The Crown Human Genome Center is also part of this site.
BioInformatics and Molecular Analysis Section
[NIH] BIMAS offers many bioinformatics tools, including DNA sequence analysis, a mirror of GeneCards, genetic linkage analysis, and more. A catalog of linkage analysis software is also provided.
[National University of Singapore] A comprehensive site providing information and multiple bioinformatic related analysis tools in areas such as phylogenetics, lab management, and metabolic pathway visualization.
Bioinformatics(Computational Biology) Group
[University of California Santa Cruz] This group is dedicated to the discovery and implementation of algorithms that facilitate the understanding of biological processes. Members study the primary (sequence), secondary (folding), and tertiary (3-dimensional) structures of DNA, RNA, and protein sequences. A number of servers and databases in these areas are provided, as well as educational materials.
[UCSD San Diego Supercomputer Center] The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. 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 Structure and Modelling Group
[University College London] The BSM group brings together people who derive protein and carbohydrate structure information using crystallography or NMR, those who manage databases of this information, and analysts and modellers who examine these structures to try to derive principles of protein folding. Services are offered in the areas of protein sequence and stucture analysis. The group is the home of the CATH protein structure classification database.
Computer based biological research via the internet. Bionatigator is a virtual bioinformatics workspace that puts a comprehensive range of internet-delivered research tools into thehands of biologists. You control your data, your analyses and youroutput, in real time and reproducibly. Running programs on BioNavigator is fee based.
The Brutlag Bioinformatics Group
[Stanford University] This group is interested in theproblems of predicting biological function of genes and proteins from their primary sequence (sometimes known as functional genomics), predicting structure of protein and DNA from its sequence, and understanding how and when genes are expressed. This site links to tools being developed toward these interests.
[Celera] Celera Corporations scientific home page that provides Celera and related biotechnology news and password access to the Celera Discovery System of genomic databases and analysis tools.
Center for Biological Sequence Analysis
[Technical University of Denmark] CBS conducts basic research in bioinformatics. It offers a number of nucleotide and protein prediction (from sequence) servers, other tools, and “value-added” datasets.
Center for Molecular Modeling
[NIH] CMM is a major supplier of molecular modeling resources andexpertise to the NIH research community. The site contains many annotated links to bioinformatics resources and tutorials.
Centre for Molecular and Biomolecular Informatics
[Univ. of Nijmegen] Information on multiple bioinformatics related services, research, and program courses at this center.
Comparative RNA Web Site
[University of Texas] A comprehensive site with information on RNA including methods in structure prediction, RNA sequence/structure database, RNA structure information, RNA structure analysis, and rRNA structure-based phylogeny.
[Oak Ridge National Laboratory] We conduct genetics research and system development in genomic sequencing, computational genome analysis, computational protein structure analysis, high-performance biocomputing, bioinformation systems, biosystems modeling, and genetics information management.
Computational Biology and Informatics Laboratory
[University of Pennsylvania] Multiple bioinformatics related tools and databases. The site also includes information about related degree programs and UPenn.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
CUBIC: Columbia University Bioinformatics Center
CUBIC contains a wealth of services, databases, articles and their data sets, and annotated bioinformatics links. It is the current home of PredictProtein and other services for protein analysis.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
DDL – Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences. This downloadable package also has special functions for EST and SAGE handling and analysis.
[European Molecular Biology Network – Swiss Node] This site provides DNA and protein sequence analysis tools, sequence alignment tools, and other bioinformatics tools. It also provides numerous links to related information, courses, universities, and documentation.
[Swiss Institute of Bioinformatics] The EXPASy “server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.” This site contains links to databases, tools and software packages, education and services, documentation, lists of links to molecular biology resources, links to major molecular biology servers, and local links.
[Nature Technology Corporation] A comprehensive site with links to information and resources in biotechnology and bioinformatics. The large number of resource categories include academic sites, conferences, employment, genomics, proteins, grants & contracts, intellectual property, methods & protocols, software, and venture capital.
GeneCensus Genome Comparisons
[Yale University] This site provides genome and phylogenetics related information, databases, and services for many classes of organisms, mainly microscopic.
[European Bioinformatics Institute] “GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases.”