Indexes of BioScience-Related Services

• All the Virology Servers in the World
• Art's Biotechnology Resource
• Scott's Botanical Links
• Biology Links – Harvard Dept. of Molecular and Cellular Biology

Molecular Biology www Servers

• Expasy Molecular Biology Server
• Human Genone Project Information
• HUM-MOLGEN Communication Forum
• Institute for Molecular Virology (U of Wisconson - Madison)
• RNA World

Organism & Organelle-Specific Databases

Human

• CEPH - Human Genotype Database
• Human Chromosome 1 Database
• Human Genome Project Database
• Human Mitochondrial Genome Database

Fish

• Zebrafish Information Network (ZFIN)

Insect

• Arabinet (AtDB)
• Mosquito Genomics
• FlyBase

Mouse

• Jackson Labs
• Mouse Genome Database
• Portable Dictionary of the Mouse Genome

Organelle

• GOBASE
• MitBASE
• MitoDat

Plant

• Arabidopsis thaliana database – TIGR
• CropNet
• INE- Rice
• MaizeGDB
• Zea Mays - TIGR

Prokaryote

• E. coli Genetic Stock Center
• CyanoBase
• EcoGene
• EMGlib
• NRSub - Bacillus subtilis genome
• Phytophthora Functional Genomics Database
• TIGR Microbial Database

Worm

• Caenorhabditis Genetics Centre
• C. elegans Worm Server
• Filarial Genome Network
• ACeDB

Yeast

• Sacchromyces Genome Database
• Saccharomyces Protein Structural Info
• Schizosaccharomyces pombe Genome Project

Viral

• HIV
• HPVSD - Human Papillomavirus Sequence Database
• World Health Organization Malaria Database

Sequence, Structure & Function Related Databases

Combined Databases

• Entrez
• Atlas
• BLAST (GenBank/EMBL/SwissProt/PIR)
• BLAST2 at EMBL (GenBank/EMBL/SwissProt/PIR)
• Munich Information Center for Protein Sequences
• WWW-Query (EMBL/Genbank/NRSub/Hovergen/HIDB)
• SRS EBI (SwissProt/PIR/EMBL/TREMBL/Prosite/BLOCKS/Medline/Rebase/DBEST + others)

Nucleic Acid Databases

• DNA Data Bank of Japan
• EMBL
• NCBI Genbank
• Nucleic Acid Structure Database
• TIGR Gene Indices
• Unigene

Comparative Genomics

• Clusters of Orthologous Groups (COG)

Gene Expression

• ASDB
• Axeldb
• dbCFC - Cytokine Family EST Database
• FlyView
• Gene Expression Database (GXD)
• Kidney Development Database
• MAGEST - Ascidian (Halocynthia roretzi) gene expression
• Mouse Atlas & Gene Expression Database
• Tooth Development Database
• TRIPLES - Transposon-Insertion Phenotypes, Localization and Expression in Saccharomyces

Gene Identification and Structure

• Ares Lab Intron Site - Yeast Spliceosomal Introns
• COMPEL - Composite Regulatory Elements
• CUTG - Codon usage tables
• EID - Protein-coding, intron-containing genes
• EPD - Eukaryotic POL II promoters
• ExInt - Exon-intron structure of eukaryotic genes
• IDB/IEDB - Intron sequence and evolution
• PLACE - Plant cis-acting regulatory elements
• TRRD- Regulatory regions of eukaryotic genes
• YIDB - Yeast nuclear and mitochondrial intron sequences

Genetic Maps

• GeneMap - International Radiation Mapping Consortium Human Gene Map
• GDB - Human genes and genomic maps
• HuGeMap - Human genome genetic and physical map data
• IXDB - Physical maps of human chromosome X
• Radiation Hybrid Database - Radiation hybrid map data

Mutation Databases

• Online Mendelian Inheritance in Man (OMIM)
• Androgen Receptor Gene Mutations Database
• Asthma and Allergy Database
• Asthma Gene Database
• Atlas of Genetics & Cytogenetics in Oncology & Hematology
• BTKbase - Mutation registry for X-linked agammaglobulinemia
• Cytokine Gene Polymorphism Database
• Database of Germline p53 Mutations
• dbSNP - Single nucleotide polymorphisms
• GRAP Mutant Database - Family A G-Protein Coupled Receptors (GRAP)
• Haemophilia B Mutation Database
• HGBASE - Intragenic Sequence Polymorphisms
• HIV-RT
• Human Gene Mutation Database (HMGD)
• Human PAX2 Allelic Variant Database
• Human PAX6 Allelic Variant Database
• Human Type I & Type III Collagen Mutation Database
• HvrBase - Primate mtDNA control region sequences
• IARC p53 Database
• KinMutBase - Disease-causing protein kinase mutations
• NCL Mutations - Neuronal ceroid lipofuscinoses (NCL) genes
• p53 Databases
• PAHdb - Phenylalanine hydroxylase locus
• PMD - Protein mutant data
• RB1 Gene Mutation Database
• SV40 Large T-Antigen Mutant Database

Pathology Databases

• FIMM - Functional molecular immunology
• Mouse Tumor Biology Database (MTB)
• PEDB - Sequences from prostate tissue and cell type-specific cDNA libraries

Protein Databases

• AAA Protein Superfamily Database
• Androgen Receptor Gene Mutation Database
• AARSDB - Aminoacyl-tRNA synthetase sequences
• Brenda ( The Comprehensive Enzyme Information System )
• COPE - Cytokines Online Pathfinder Encyclopedia
• DExH/D Family Database - DEAD-box, DEAH-box and DExH-box proteins
• Endogenous GPCR List
• Enzyme Nomenclature Database
• ESTHER - Esterases and hydrolase enzymes and relatives
• FUNPEP - Low-complexity or compositionally-biased protein sequences
• GPCRDB - G protein-coupled receptors
• Histone Sequence Database
• HIV Molecular Immunology Database
• Homeobox Page
• Homeodomain Resource
• HUGE - Large (>50 kDa) human proteins and cDNA sequences
• IMGT - Immunoglobulin, T cell receptor and MHC sequences
• InBase - Intervening protein sequences (inteins) and motifs
• Kabat Database - Sequences of proteins of immunological interest
• LGIC - Ligand-gated ion channel sequences, alignments and phylogeny
• Membrane Protein Database
• MEROPS - Peptidase sequences and structures
• MHCPEP - MHC-binding peptides
• Molecules-R-Us PDB (NIH)
• Munich Information Center for Protein Sequences (MIPS)
• NRR - Steroid and thyroid hormone receptor superfamily
• ORDB - Olfactory Receptor Database
• PDB (Brookhaven)
• PhosphoBase - Protein phosphorylation sites
• PIR - Protein Information Resource
• PKR - Protein Kinase Resource
• Prolysis - Proteases
• Receptor Database (RDP)
• Ribonuclease P Database
• SENTRA - Sensory signal transduction proteins
• SWISS-PROT (Protein database)
• TFD - Transcription factors and gene expression
• TRANSFAC - Transcription factors and binding sites
• Wnt Database - Wnt proteins and phenotypes

Protein Sequence Motifs

• PROSITE - Protein patterns and profiles
• Pfam - Sequence alignments and Markov models of protein domains
• O-GLYCBASE - Glycoproteins and O-linked glycosylation sites
• PIR-ALN - Protein sequence alignments
• PRINTS - Protein sequence motifs and signatures
• ProClass - Families defined by PROSITE patterns and PIR superfamilies
• ProDom - Protein domain families
• ProtoMap - Automated hierarchical classification of SWISS-PROT proteins
• SBASE - Annotated protein domain sequences
• SMART - Signaling domain sequences
• SYSTERS - Protein clusters

Protein Structure

• ASTRAL - Analysis of protein structures and their sequences
• CATH - Hierarchical classification of protein domain structures
• BioMagResBank - NMR spectroscopic data from proteins, peptides and nucleic acids
• Database of Macromolecular Movements
• Decoys 'R' Us - Computer-generated protein conformations based on sequence data
• HSSP - Structural families and alignments
• IMB Jena Image Library
• LPFC - Library of protein family core structures
• MMDB - All three-dimensional structures, linked to NCBI Entrez system
• MODBASE - Comparative protein structure models
• NDB - Nucleic acid-containing structures
• PDB - Structure data
• PDB-REPRDB - Representative protein chains, based on PDB entries
• PRESAGE - Protein structures with experimental and predictive annotations
• Protein Motions Database
• ProTherm - Thermodynamic data for proteins
• Protein Structure Prediction Database
• RESID - Protein structure modifications
• SCOP - Familial and structural protein relationships

Proteome Resources

• AAindex - Physicochemical properties of peptides
• REBASE - Restriction enzymes and methylases
• SWISS-2DPAGE - 2D-PAGE images and reference maps

RNA Sequences

• 5S Ribosomal RNA Databank
• ACTIVITY:  Functional DNA/RNA site sequences
• Collection of mRNA-like non-coding RNAs
• Database on the Structure of Large Subunit Ribosomal RNA
• Database on the Structure of Small Subunit Ribosomal RNA
• Guide RNA Database
• Intronerator
• Non-canonical Base Pair Database
• Plant mitochondrial tRNAs and tRNA genes
• Pseudobase - Information on RNA pseudoknots
• Ribosomal Database Project (RDP)
• RNA Modification Database
• SELEX_DB
• Small RNA Database
• SRPDB - Signal recognition particle RNA, protein, and receptor sequences
• tmRDB - tmRNA (10Sa RNA) sequences
• tmRNA - tmRNA (10Sa RNA) sequences
• tRNA Sequences
• UTRdb - 5' and 3' UTRs of eukaryotic mRNAs
• Viroid and Viroid-Like RNA Database

Transgenics

• Cre Transgenic Database
• Transgenic/Targeted Mutation Database

Database Notification Services

• SWISS-Shop (SwissPROT)

Image Databases

• EMBL Virus Structures
• Image Library of Biological Macromolecules
• Molecules-R-Us (NIH)
• SWISS-3DIMAGE Annotated 3-D Images
• Visualizations of Viruses

Database Indexes

• DBCAT - Index of Molecular Biology Databases

Database Sources (downloadable images of sequence databases)

• Human STS - Human Physical Mapping Project (Whitehead Institute)
• Protein Information Resource (NBRF)
• PRINTS - Protein Motif Fingerprint Database
• TREMBL Translated Protein Sequence Database (EBI)

Nucleic Acid & Protein Sequence Analysis

• ALIGN (Pairwise Sequence Alignment)
• Cytogenetic Correspondence Linkage Map Note: Requires Java-compliant browser
• Gene-map Homology Search
• Genome Navigator - Interactive Genome Viewer
• INCA Recursive BLAST database search (Requires Java)
• NCBI ORF (Open Reading Frame Finder)
• Pattern analysis at PBIL
• PEDANT - Protein Extraction, Description, and ANalysis Tool
• SAPS (Statistical Analysis of Proteins)
• SEALS System for Easy Analysis of Lots of Sequences (NCBI)
• SeqPup - Sequence Editor and Analysis
• TMpred (Prediction of Transmembrane Regions)
• WebCutter (Restriction Maps)

Nucleic Acid & Protein Microarray Links

• ARGUS - Harvard University
• ArrayExpress - European Bioinformatics Institute
• BASE - BioArray Software Environment
• Clinical Proteomics Research Map
• EBI - European Bioinformatics Institute
• ExpressDB - Harvard University
• GenomeWeb - Rosalind Franklin Centre for Genomeics Research
• GEO - Gene Expression Omnibus - NCBI
• HuGE Index
• MAD Microarray Database - Jackson Laboratory
• MAPS - NIEHS Microarray Group
• MAXD - University of Manchester
• M-CHIPS - German Cancer Research Center
• MGED - Microarray Gene Expression Data Society
• Microarrays.org - UCDF
• National Human Genome Research Institute
• NCGR - National Center for Genome Resources
• NOMAD - UCSF & LBNL
• ONCOMINE - Cancer Microarray Database
• PUMA - Princeton University MicroArray Database
• RAD3 - RNA Abundance Database - University of Pennsylvania
• READ - RIKEN Expression Array Database
• Stanford MicroArray Database
• Stanford Protein Microarray Site
• TeleChem International - Microarray Electronic Library
• TIGR - The Institute for Genomic Research
• University of North Carolina Microarray Database
• Yale Microarray Database

Conferences

• Cold Spring Harbor Courses and Meetings
• Gordon Research Conferences
• Keystone Symposia

Educational Resources

• The Biology Project Web Biology Course (U of Arizona)
• BIODIDAC Resources for Biology Teaching
• Cell Biology Education
• Clinical Case Tutorials in Biochemistry
• Fundamentals of Sequence Analysis (Caltech)
• Kimball's Biology Pages - Definitions for Biology
• MendelWeb Mendelian Genetics Tutorial

Miscellaneous Tools and Web Sites

• American Type Culture Collection
• CCRC(CarbBank) - Complex Carbohydrate Structural Database
• Cell Line Database
• ChemJobs.Net
• Coriell Cell Repositories
• Database of Genome Sizes (DOGS)
• DBGET (Integrated Database Retrieval System)
• HIC-Up - Hetero-Compound Structural Database
• Image Library of Biological Macromolecules
• IMGT – Immunogenetics Database
• Institute for Laboratory Animal Research - (ILAR)
• LIPIDAT
• Molecular Probe Database
• Mouse Knockout and Mutation Database
• Nobel Prize Internet Archive
• Nobel e-Museum

Trade Publications, News Services and Buyer's Guides

• American Biotechnology Laboratory
• American Laboratory News
• BioArray News
• BioCommerce Week
• BioCompare
• BioInform
• BioScience Technology
• BioSpace
• Biotechniques
• Drug Discovery & Development
• Genetic Engineering News
• Genomics & Proteomics
• GenomeWeb
• International Biotechnology Laboratory
• International Laboratory News
• Lab Velocity
• ProteoMonitor
• R&D Research and Development
• The Scientist

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TRADEMARKS & PATENTS

 

• Ficoll-Paque is a registered trademark of Amersham Pharmacia Biotech, Inc.
• Macintosh is a registered trademark of Apple Computer.
• Texas Red and SYBR are trademarks of Molecular Probes.
• Phycoerythrin (PE) conjugates allophycocyanin: US Patent No. 4,520,110; 4,859,582; and 5,055,556; European Patent No. 76,695; Canadian Patent No. 1,179,942
• Carbocyanin (Cy): US Patent No. 5,268,486; 5,486,616; 5,569,587; 5,569,766; and 5,627,027
• PCR is a process patented by Hoffman-LaRoche: US Patent No. 4,683,195
• * AFC was developed by, and ChromoFluor96™ is a trademark of Enzyme Systems Products division of ICN Biomedicals, Inc. (patent pending).
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