Genomes &
Machines
Reviews, databases and general
resources on genomics and bioinformatics systems.
The purpose of these pages is to provide an overview of the rapidly evolving
field of bioinformatics. We define bioinformatics as a discipline that
generate computational tools, databases and methods to support genomic,
molecular and medical research. This research basically comprises the
study of DNA structure and function, gene and protein expression, protein
production, structure and function, genetic regulatory systems, etc.
In this page you will find links to the most representative genomic databases
and tools, tutorials, data and software providers, public and private research
centres, relevant paper references, reviews on articles and products, etc.
Contents
Genomic
and molecular biology databases
Genome Mapping and Sequence
Repositories
- Arabidopsis Genome Resource(AGR)
- The Genome Database:
it contains all known nucleotide and protein sequences.
- GenBank: it contains all known
nucleotide and protein sequences.
- EMBL Nucleotide Sequence
database: it contains all known nucleotide and protein sequences.
- TIGR Gene
Indices: gene-oriented clusters.
- DNA Data Bank of
Japan (DDBJ): it contains all known nucleotide and protein
sequences.
- UniGene:
gene-oriented clusters.
- Genome
Sequence Database (GSDB): it contains all known nucleotide and protein
sequences.
- Blocks:
Database of Highly-Conserved Protein Regions.
Comparative Genomics
Gene
expression data
Gene Identification and
Structure
- Ares Lab
Introm Site: Yeast spliceosomal introns.
- COMPEL:
Composite regulatory elements.
- CUTG:
Codon usage tables.
- EID:
Protein-coding, intron-containing genes.
- EPD: The
Eukaryotic Promoter Database.
- ExInt: Exon/Intron
database.
- IDB/IEDB: Intron
sequence and evolution databases.
- PLACE: Database of Plant
Cis-acting Regulatory DNA Elements.
- PlantCARE: Database of
Plant Cis-acting Regulatory DNA Elements.
- TransTerm: Database of
messenger RNA components and signals.
- TRRD: Transcription
Regulatory Regions Database.
- YIDB:
Yeast Intron DataBase.
Genetic Maps
- GeneMap'99: Gene Map of the
Human Genome
- G3-RH:Stanford G3 and
TNG radiation hybrid maps.
- GB4-RH: Genebridge4
(GB4) human radiation hybrid maps - Sanger Centre.
- GDB: Human genes and
genomic maps.
- DRESH: Map
positions of human genes homologous to Drosophila melanogaster genes.
- GenAtlas:
Human genes, markers and phenotypes.
- HuGeMap: Human genome
map.
- IXDB:
Physical map of human chromosome X, MP Institute - Berlin.
- Radiation Hybrid Database:
Radiation hybrid map data.
Genomic Databases
Molecular Interactions
- DRC:
Ribosomal crosslink data.
- DIP: Catalog of
protein-protein interactions.
- DPInteract:
Binding sites for Escherichia coli DNA-binding proteins.
Metabolic and regulatory pathways, enzymes
and nomenclature.
Mutation Databases
Pathology databases
- FIMM:
Functional molecular immunology data (diseases, antigens, peptides and HLA
binding sites)
- Mouse
Tumor Biology Database (MTB): Mouse tumor names, classification,
incidence, pathology, genetic factors
- PEDB: Sequences from
prostate tissue and cell type-specific cDNA libraries
Protein databases
- AARSDB:
Aminoacyl-tRNA synthetase sequences
- BRENDA
- enzyme database
- CluSTr - a database of clusters
of SWISS-PROT+TrEMBL proteins
- DAtA:
Annotated coding sequences from Arabidopsis
- DExH/D Family
Database: DEAD-box, DEAH-box and DExH-box proteins
- Endogenous GPCR
List: G protein-coupled receptors; expression in cell lines
- ESTHER:
Esterases and [alpha]/[beta] hydrolase enzymes and relatives
- FUNPEP:
Low-complexity or compositionally-biased protein sequences
- GenProtEC: Escherichia coli
genes, gene products and homologs
- GPCRDB: G
protein-coupled receptors
- Histone Sequence
Database: Histone and histone-fold sequences and structures
- HIV Molecular Immunology
Database: HIV epitopes
- The Homeodomain
Resource
- Homeobox
Page: Information relevant to homeobox proteins,
classification and evolution
- Homeodomain
Resource: Homeodomain sequences, structures, and related genetic and
genomic information
- 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: Membrane protein sequences, transmembrane regions
and structures
- MEROPS: Peptidase
sequences and structures
- MHCPEP: MHC-binding
peptides
- NRR: Steroid
and thyroid hormone receptor superfamily
- Olfactory Receptor
Database: Sequences for olfactory receptor-like molecules
- ooTFD: Transcription factors and
gene expression
- Peptaibol:
Peptaibol (antibiotic peptide) sequences
- PhosphoBase:
Protein phosphorylation sites
- PKR:
Protein kinase sequences, enzymology, genetics, and molecular and structural
properties
- PPMdb:
Arabidopsis plasma membrane protein sequence and expression data
- Prolysis:
Proteases and natural and synthetic protease inhibitors
- PROMISE: Prosthetic
centers and metal ions in protein active sites
- Protein Information
Resource (PIR): Non-redundant protein sequence database
- Receptor Database
(RDP): Receptor protein sequences
- Ribonuclease P
Database: RNase P sequences, alignments and structures
- SENTRA:
Sensory signal transduction proteins
- SWISS-PROT/TrEMBL: Curated
protein sequences
- TIGRFAMs - a protein family
resource for the functional identification of proteins
- TRANSFAC:
Transcription factors and binding sites
- Wnt
Database: Wnt proteins and phenotypes
Protein Sequence Motifs
- BLOCKS: Protein sequence motifs
and alignments
- PROSITE:
Biologically-significant protein patterns and profiles
- Pfam:
Multiple sequence alignments and hidden Markov models of common protein
domains
- O-GLYCBASE:
Glycoproteins and O-linked glycosylation sites
- PIR-ALN:
Protein sequence alignments
- PRINTS:
Protein squence 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: Signalling domain
sequences
- SYSTERS:
Protein clusters
Proteome Resources
RNA Sequences
Retrieval Systems and Database
Structure
- 3Dee - A
Database of protein Domain Definitions -
http://circinus.ebi.ac.uk:8080/3Dee/help/help_intro.html
- KEYnet: Keywords
extracted from EMBL and GenBank
- Virgil:
Database interconnectivity
- Gene-e-Us.org: personalised, web
based genomic information acquisition tool
- GIST: A web tool for
collecting gene information
Structure
- PDB:
Structure data determined by X-ray crystallography and NMR
- CATH: Hierarchical
classification of protein domain structures
- SCOP: Familial and
structural protein relationships
- ASTRAL: Analysis of protein
structures and their sequences
- BioImage:
Searchable database of multi-dimensional biological images
- BioMagResBank: NMR
spectroscopic data from proteins, peptides and nucleic acids
- CSD: Crystal structure
information for organic and metal organic compounds.
- Database of Macromolecular
Movements: Descriptions of protein and macromolecular motions,
including movies
- Decoys 'R' Us:
Computer-generated protein conformations based on sequence data
- HIC-Up:
Structures of small molecules ('hetero-compounds')
- HSSP: Structural families
and alignments; structurally-conserved regions and domain architecture
- IMB Jena
Image Library: Visualization and analysis of three-dimensional
biopolymer structures
- ISSD: Integrated sequence
and structural information
- 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-REPRDB:
Representative protein chains, based on PDB entries
- PRESAGE: Protein structures with
experimental and predictive annotations
- ProTherm:
Thermodynamic data for wild-type and mutant proteins
- RESID:
Protein structure modifications
Transgenics
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General
Resources
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Representative public research
centres, data and
tools.
Research centres in the U.S.A
Europe
Other centres
- Centre for DNA
Fingerprinting and Diagnostics, EMBnet - India
- Centre of
Bioinformatics - Peking University, China
- Centro de
Ingenieria Genetica y Biotecnologia, Cuba
- Instituto de Bioquimica
y Biologia Molecular - IBBM (EMBnet - Argentina)
- Genome Sequence
Centre, Vancouver, Canada
- South African
National Bioinformatics Institute
- Bioinformatics
Centre - National University of Singapore
- Bioinformatics
Centre (DIC)- University of Pune, India
- ONSA, Xylella
fastidiosa Genome
Project, São Paulo, Brazil.
- Weizmann
Institute of Science, Israel.
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Database,
software, hardware
and service providers
- Affymetrix: Expression chips,
analysis and services.
- Agilent Technologies:
Gene expression analysis systems including hardware and software.
- BioResearch
Ireland: national agency commercialising biotechnology
- Celera: A division of PE Corp founded
to rapidly sequence the human and other genomes, with the intent to supply
high value-added genomic data to life science collaborators.
- Compaq: It has a strategic alliance
with Celera to provide integrated bioinformatics harware, software, networking
and service solutions.
- Compugen: Internet portal,
proprietary and collaborative gene discovery.
- CuraGen: Conducts project driven
genomic R&D for propriety use and in collaboration with life science
partners.
- Deltagen: Functional genomics.
- Digital Gene Technologies: TOGA system
correlates expression with anatomy.
- DNA Sciences: Gene Trust patient
database.
- DoubleTwist.com: Internet portal
business model, on-line access to bioinformatics tools, databases and other
products.
- eBioinformatics: Variety of
web-based bioinformatics tools and databases.
- First Genetic Trust: Database,
patient information encryption.
- Gemini Genomics: Genotyping,
SNPs.
- Genaissance: Population
genomics, "personalized medicine".
- GeneLogic: Gene expression
database products.
- Genomica: Enterprise-wide
bioinformatics systems and services.
- Genomics Collaborative: SNP
genotyping.
- Genomics Institute (a division of Novartis): genomics, proteomics, mouse
genetics.
- Genomic Solutions:
Biochips.
- Human Genome Sciences: Sequencing,
expression analysis, proteomics, clinical testing.
- IBM: Resarch into high value-added data
mining and protein structure determination methods. "Blue Gene" supercomputer.
- Incyte: Bioinformatics database
company, gene expression, proteomics and other data analysis tools.
- Informax: Desktop and
enterprise-wide bioinformatics products.
- Integrated Genomics:
Microbial genomes.
- LabBook: genomic XML browser.
- Lexicon Genetics: Biochips.
- Lion Bioscience:
Enterprise-wide bioinformatics systems and services, technology for
proprietary R&D.
- Molecular Mining: Data
mining algorithms for gene expression analysis.
- Motorola Biochip:
Expression arrays.
- Molecular Simulations: Software tools.
- Myriad Genetics: Therapeutic
and diagnostic product development via genomic and proteomic methods.
- Nanogen: biochips.
- Neomorphic: Bioinformatics tools
to mine and visualize genomic information.
- Netgenics: Enterprise-wide
bioinformatics systems and services.
- Orchid Bioscience: SNP
genotyping.
- Oxford Molecular:
Business model that includes bioinformatics and related fields of
cheminformatics and computational chemistry.
- Paracel: Computer hardware/software
designed to accelerate bioinformatics algorithms.
- Partek: Analysis of microarray data.
- PE Biosystems: A division of PE Corp,
offers software products to life sciences.
- Prospect Genomics:
Structure prediction.
- Rosetta Inpharmatics: Gene expression
data acquisition for drug discovery applications.
- Senomyx: Smell & taste genes.
- Silicon Genetics: Tools for gene
expression analysis and visualization.
- Silicon Graphics: SGI systems support
bioinformatics software applications.
- SpotFire: Data visualization
software for gene expression.
- Structural Bioinformatics:
Bioinformatics tools and databases with special focus on protein structural
information.
- Structural GenomiX: Proteomics,
structure prediction.
- Sun Microsystems: Sun systems support
bioinformatics software applications.
- Syrrx: Protein structure prediction.
- TimeLogic: Computer
hardware/software designed to accelerate bioinformatics algorithms.
- Zyomyx: Protein biochips.
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Getting connected to bioinformatics: special
issues, courses andtutorials
- A list of
bioinformatics courses
- BIOML: XML language, designed to be
used for the annotation of biopolymer sequence information
- Canadian Bioinformatics Resource
- CNN.com
Special:Blueprint of the body (overviews, essays and interviews)
- Cold Spring
Harbor short courses
- GEML: an
Extensible Markup Language (XML)-based tag set, developed by Rosetta
Inpharmatics.
- Gold: genomes
online databases
- VIRTUAL
Bacteria ID LAB: Howard Hughes Medical Institute (HHMI)
- Human Genome Organisation
- IBM
Computational Biology Center
- IEEE Computing in Science &
Engineering: Special issue on computational biology (May-June, 1999).
- IEEE
Engineering in Medicine and Biology: Genomes & Machines (special issue
on "Computing Life" with Bioinformatics, Jul/Aug 2001, Vol.20, Issue 4)
- IEEE Spectrum (Vol. 37, Number
11, Nov. 2000): Introduction to genome sequencing and analysis.
- Incyte Genomics (technologies and
tutorials)
- Kyoto Encyclopedia of Genes &
Genomes
- MAML: Microarray Markup
Language
- National Center for Biotechnology
Information
- National Center for Genome Resources
- Nature: Special issue on the human
genome, Vol. 409, pp.813-958, (15/02/01)
- Nature Genome Gateway:
including a special section to mark the publication of the initial
sequencing and analysis of the human genome.
- Nature insight on functional
genomics: Nature, Vol. 405, (15/06/00), pp. 819-865.
- UCLA Bioinformatics
Institute
- Science: Special issue on the
human genome, Vol. 291, (16/02/01).
- Science
Functional Genomics: A collection of resources related to the human genome
sequence.
- S-STAR.org is an alliance between 6
universities in 5 continents, bioinformatics education on-line
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Proteomics:
general information
and opportunities
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Ethical and legal issues
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Journals and publications
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Conferences
and events
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Created and maintained by Francisco Azuaje
Department
of Computer Science, The University of Dublin -
Trinity College.