ACNUC is a retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence database NBRF/PIR. Now, it is also possible to query a merging of the two protein collections SWISS-PROT and TREMBL with the sequence database management system ACNUC

A general purpose application wrapper based on CORBA and Java, with a focus on sequence analysis tools in bioinformatics. Still in alpha status, but freely available for anyone who wants to try it.

CLUSTAL W is a program for multiple sequence alignment which includes several modifications to improve results for the alignment of divergent protein sequences.

DRAGON is a protein modelling tool that attempts to predict the tertiary structure of a small soluble protein, given its sequence, the secondary structure and possibly a set of interresidue distance restraints.

The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data.

GCUA is designed to calculate various parameters that might be relevant in assessing the codon usage patterns of a group of genes.

GeneDoc is a fully featured Multiple Sequence Alignment Editor and Shading Utility.

MitoProt II provides the possibility to predict mitochondrial proteins harbouring targeting sequences.

MODELLER is most frequently used for homology or comparative modeling of protein three-dimensional structure: the user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a full-atom model.

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids.

The NetOGlyc 2.0 WWW server is a prediction server of mucin type O-glycosylation sites in mammalian proteins.

PEDANT stands for Protein Extraction, Description, and ANalysis Tool and is a software system for completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes.

PROCRUSTES 4.01 is geared towards computational support of experimental gene identification and annotation-quality gene predictions.

ProMSED2 (Protein Multiple Sequence EDitor-2) is a Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis.

Sequin is the latest multi-platform (Mac/PC/Unix) stand-alone software tool developed by the NCBI for submitting entries to the EMBL, GenBank, or DDBJ sequence databases.

SRS (Sequence Retrieval System) is an indexing system which gives access to virtually all databanks available in a text (ASCII) format. An important feature is its ability to combine all indexed databanks into a network where new ways of linking information from different sources can be explored.

TESS (Transcription Element Search Software) is a set of software for locating and displaying transcription factor binding sites in DNA sequence.

VMD is designed for the visualisation and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure.

WebIn is the new WWW Sequence Submission Tool for submitting nucleotide sequence data and associated biological information to the EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI).

WPDB is a protein structure database search and display tool for use on Windows 3.1, Windows 95 and Windows NT platforms. WPDB is useful for detailed analysis of a single structure or comparative analysis of two or more structures.

XYLEM is a package of tools designed to exploit the Unix environment to enable the user to identify, extract and manipulate data from major databases such as GenBank and PIR.

Release 51 of the EMBL Nucleotide Sequence Database, with a growth of 18% over last release. Now includes cross-references to the MENDEL database of plant gene nomenclature.

GeNet is a specialised database which contains the information on functional organisation of regulatory genes networks acting at embryogenesis.

GenPept is a searchable protein database containing known or potential coding regions identified by GenBank sequence submitters.

The database is specifically devoted to artificial mutations introduced into known sequences of ion channels.

PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of OWL.

The ProClass Protein Family Database is a non-redundant database organised according to family relationships as defined collectively by PIR superfamilies and ProSite patterns.

The Protein Domain database, ProDom, release 34, has been constructed by clustering homologous segments derived from 53145 non-fragmentary sequences present in SWISS-PROT 34. It provides 18086 multiple alignments and consensus sequences for homologous domain families.

Following a termination of a contract with Human Genome Sciences, Inc., TIGR releases sequence data of twelve different organisms (a total of 40 Mb) to the public. 

TRANSFAC is a database on eukaryotic cis-acting regulatory DNA elements and trans-acting factors. It covers the whole range from yeast to human.

A physical map of the mouse genome consisting of 10,000 markers screened against a mouse YAC library.