ALIGN at EERIE-Nimes, France -- ALIGN allows you to choose various matrices for DNA or protein-sequence alignment. It is pretty bare-bones and does not indicate what type of algorithm this alignment is based upon.

AMAS at Oxford -- Analyses of Protein Multiple-Sequence Alignments: used to highlight unusual or interesting amino-acid substitution patterns important in the design of mutagenesis experiments.

BCM Search Launcher at Baylor College of Medicine -- The BCM Launcher is an on-going project to create a WWW utility which can provide a single interface to access molecular biology analysis-services. These interfaces are ordered by function. This site is extremely comprehensive; a must see!

Biological Information at Agricultural Biotechnology Center, Hungary -- This site contains many links, especially in plant biology.

Biological Units at Brookhaven National Laboratory -- Contains the expanded PDB entries with coordinates for the full biological units (the functional molecule). Very useful but NOT for the faint of heart.

Biologist's Control Panel at Baylor College of Medicine -- An extremely comprehensive guide to searching tools for biological databases. Includes traditional databases such as GenBank, GDB, Genethon, SWISS-PROT, etc. as well as some other interesting sources of data.

BioMagResBank at NIH Molecular Modeling -- The BioMagResBank is an NMR-derived protein structure database created and maintained at the University of Wisconsin, Madison. The WWW front-end was created by the BIMAS section of the NIH and allows you to query by author, protein, protein variants, shift assignments and also perform homology searches with FASTA-formatted sequences.

BLOCKS at Fred Hutchinson Research Center -- BLOCKS compares protein or DNA sequences to mutiply aligned, ungapped segments which correlate with the most highly conserved regions of proteins. BLOCK enables you to compare blocks, retrieve blocks and create new blocks. This algorithm uses the PROSITE and SWISS-PROT located at ExPASy WWW Molecular Biology Server at the University of Geneva.

BMCD at CARB, Maryland Biotech Institute & NIST -- The BMCD is a collection of crystallization conditions and crystal-data compiled from sources in the literature. It also contains the NASA Protein Crystal Growth Archive which documents crystal growth in microgravity environments.

CATH at Biomolecular Structure and Modelling Unit of University College, London -- The CATH database is a hierarchical domain classification of protein structures in the Brookhaven protein databank. All non-protein, model, and "C-alpha only" structures are not classified in CATH. Only crystal structures solved to resolution better than 3.0 angstroms are considered, together with NMR structures.

Dali at EMBL -- The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.

dbEST at NCBI -- dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.

DBGET at GenomeNet, Japan -- DBGET is an integrated database retrieval system designed at GenomeNet in Japan. It allows you to search and retrieve entries from any number of databases. This site is quite friendly and straigforward.

Entrez at NCBI -- This site allows you to search nucleotides, proteins, 3-D structures, taxonomy, genomes, and PubMed.

ENZYME at ExPaSy, Switzerland -- Repository of information for enzyme nomenclature based upon IUBMB (International Union of Biochemistry and Molecular Biology) standards. You can fetch information on enzymes by EC number (Enzyme Commission), enzyme class, description, compound, cofactor, or search comment lines.

Enzyme Structures Database at University College, London -- This site contains the known enzyme structures deposited in the PDB (Protein Data Bank) at Brookhaven National Laboratories.

FASTA at EBI -- FASTA is an alignment algorithm which allows the introduction of gaps into query sequences. Typically, FASTA is used to search the GenEMBL database.

GDB at Johns Hopkins University -- The GDB (Human Genome Data Base) provides human genome mapping information via the GDB and OMIM (Online Mendalian Inheritance in Man) databases.

Gene Finder at Baylor College of Medicine -- Looks for splice sites, putative protein coding exons and assists in model construction (gene) via exon-assembling and prediction of possible exon-exon junction positions in cDNA.

Genome Database & Centers at EERIE-Nimes , France -- A compiled list of human, mouse, vertebrate, invertebrate and other genome databases. Both compilations are quite comprehensive and give one a good flavor of what databases/services are available.

Grail at ORNL -- GRAIL and GenQuest are designed to identify protein coding regions; use gap for gene-modeling; find polyA sites, pol II promoters and CpG islands; as well as identify human repetitive DNA elements.

LFASTA at EERIE-Nimes , France -- LFASTA does similarity searches between two sequences. Output includes local alignments.

MassSearch at ETH-Zürich , Switzerland -- This site uses a form so that you can enter the proteases used on your protein. Following submission, the database-engine searches SwissProt or EMBL databases to help you identify your protein.

MGI at Jackson Laboratories -- The mouse-genome database at Jackson Laboratory is extremely comprehensive. It contains information such as markers, probes, homology and mapping data for the mouse genome. Additionally, it has numerous citations and searching-mechanisms to search for PCR primer data.

nnPredict at UCSF -- nnPREDICT uses various algorithms to return a putative secondary structure for the protein sequence entered.

NRL_3D at NBRF -- The NRL-3D database is a sequence-structure database derived from entried in the PDB at Brookhaven National Laboratory.

OMIM at NCBI -- OMIM (Online Mendelian Inheritance in Man) is the on-line version of OMIM which serves clinical medicine and the Human Genome Project. It annotates all genes and genetic disorders with the most recent genetic research and molecular information available.

OWL at Johns Hopkins University -- Updated daily, this non-redundant protein sequence database at Johns Hopkins incorporates SWISSPROT, PIR, GenBank (translations) and NRL-3D. Additionally, it has links to PIR, GenBank, EMBL, DDBJ, PDB, EC-Enzyme, PROSITE, OMIM, SWISS-2DPAGE, REBASE and Refbase.

PatScan at Argonne Nat'l Labs -- PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.

PHILIP-Bootstrapping at Institut Pasteur , France -- Analysis which calculates hypotheticla divergence between protein or nucleotide sequences based upon criteria such as protein distance, parsimony, maximum likelihood, etc.

PIR at NBRF -- Protein Identification Resource database.

PredictProtein at EMBL-Heigelberg -- The PredictProtein server allows you to use algorithms which predict secondary structure, solvent accessibility, transmembrane helices and also generate multiple sequence alignments.

Primer at Whitehead Institute, MIT -- Does a computer-aided search to determine optimal primers for your PCR reactions based upon criteria such as minimum melting temperatures, GC content, salt concentrations, etc. Very useful, very nice.

PRINTS at University College , London -- Protein Motif Fingerprint Database.

PROPSEARCH at EMBL-Heidelberg -- Common protein sequence alignment programs are at present not capable to detect functional and / or structural homologs, if the sequence identity is below the significance threshold of about 25%. PROPSEARCH was designed to find the putative protein family if querying a new sequence has failed using alignment methods. By neglecting the order of amino acid residues in a sequence, PROPSEARCH uses the amino acid composition instead.

Prosite at ExPASy , Switzerland -- PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.

Protein Data Bank at Biology Department of Brookhaven National Laboratory -- This is an archive of experimentally determined three-dimensional structures of biological macromolecules, it contains atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data.

PSSP at BCM -- Protein secondary structure predictions via SSP (Segment oriented, Secondary structure Prediction) and NNSSP (Nearest Neighbor Secondary Structure Prediction) at Baylor College of Medicine.

REBASE & REBASE WAIS search at New England Biolabs -- REBASE is a database of information regarding restriction enzymes, methylases, organism of isolation, recognition sites, cleavage sites, specificity of methylases, references and the commercial availability of these enzymes. Additionally, there are various observations noted regarding these enzymes.

SAPS at ISREC , Switzerland -- Statistical Analysis of Protein Sequences does statistical anaylses of proteins and returns output describing compositional analysis; charge distribution; scoring distribution for positive, negative, mixed and uncharged segments; charge runs and patters; distribution of hydrophobic and transmember segments; repetitive structures; multiplets; and periodicity analysis.

SBASE & SBASE Search at ICGEB , Italy -- SBASE is an annotated database of protein sequence domains which you can do BLAST searches against as well as search through various indices in SBASE.

SCOP at Cambridge , UK -- Structural Classification of Proteins database seeks to provide complete descriptions of the structural and evolutionary relationships between all proteins whose structure has been elucidated. It contains rich information on the close relatives of particular proteins and also provides a framework for future research and classification.

SNP at Washington University -- This website is designed to provide the human genetics community with access to single nucleotide polymorphism (SNPs) that have been developed as genetic markers on the human genome. The site is organized by chromosomes and cytogenetic location. Each SNP has PCR primer and conditions associated with it.

SRS at EBI -- Sequence Retrieval System allows you to search by various indices such as accession, date, definition-line, organism, authors, reference and sequence-length.

SwissProt at ExPASy , Switzerland -- SWISS-PROT is a protein sequence database which provides rich annotations for all of its entries. Examples of annotations commonly found are protein function, domain structure, post translational modifications, variants, etc.

TBASE at Johns Hopkins University -- TBASE is a searchable database which contains organized information on transgenic animals and targeted mutations developed worldwide. This also allows individual investigators to submit information to TBASE.

TFASTA at EERIE-Nimes , France -- TFASTA compares an amino-acid query sequence with every possible translation from the GenEMBL database. TFASTA is more sensitive to related BLAST algorithms because is allows the inclusion of gaps to maximize matches and minimize mismatches.

TreeGen at ETH-Zürich , Switzerland -- TREEGEN computes phylogenetic trees and optimal 2D placements based upon a submitted distance matrix (with variance matrix being optional). Options include creation of an unrooted phylogenetic tree, rooted phylogenetic tree, placement of sequences on 2D plane, values and graph of dSplits data.

ZPRED at Ludwig Cancer Research Institute -- MultPredict Secondary Structure of Multiply Aligned Sequences predicts secondary structure using physicochemical information from a set of aligned sequences and the Garnier et al (1978, J. Mol. Biol. 120) secondary structure decision constants.