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

 

25-6790 & 25-6791:

L. S. Tang et al., COUP-TFI controls Notch Regulation of Hair Cell and Support Cell Differentiation. Development, September 2006.
http://dev.biologists.org/content/133/18/3683.full

M. H. Muders et al., Expression and Regulatory Role of GAIP-interacting Protein GIPC in Pancreatic Adenocarcinoma. American Association for Cancer Research, Nov. 2006.

L. Duncan et al., Differential Expression of Unconventional Myosins in Apoptotic and Regenerating Chick Hair Cells Confirms Two Regeneration Mechanisms. Comparative Neurology. Dec. 2006, 691-701. http://onlinelibrary.wiley.com/doi/10.1002/cne.21114/full

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• 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
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