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Bioinformatics
Global Bioinformatics Directory

Headlines
Online Database Links
Supercomputers links..
[Prokaryotic Genomes][Genomic Databases of Model Organisms][Genome
Databases][Human and Mouse Genome Comparisons][Gene and Genome
Chemoinformatics links..
Relationship and Proteome Analysis][Metabolism and Regulation,Functional
Genomics][Gene Nomenclature, Functional Characterization,and Genome
Neuroinformatics links..
Database Development][RNA Databases][Mutation Databases][Immunogenic
and Receptor Databases][Protein Structural Databases][Database of Patterns
Medicalinformatics links... and Sequence of Protein Families]

Geoinformatics links...

Bioinformatics
Bioinformatics Search
A computerized store
house of data that
provide a standardized Section Links
way for locating,
adding, and changing NCBI
data. EMBL
DDBJ
PDB
1. 1. Object-oriented databases
Unlike rational databases ,uses tubular structures , object MMDB
oriented databases attempt to model the structure of a given SCOP
data set that as closely as possible. In doing so , object-
CATH
oriented databases tend to reduce the appearance of duplicated
data and the complexity of query structure often found in TIGR
rational database PIR
2. Rational databases Bioinformatics
Organizes informations into tables where each column Databases
represents the field of informations that can be stored in Alignments
a single record. Each row in the table corresponds to a Journals
single record. A single database can have many tables Software Links
and a query languages is used to access the data. Others

Primary Database

1. Genome Database
1. Sequence Database
2. Structural Database
2. Protein Database
1. Structural Database
3. Complex Database
1. Protein Nucleic acid Complex Database

Secondary Database

1. Protein Database
1. Sequence Database
2. Complex Database
1. Protein Nucleic Acid Interaction Database

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Definitions

Primary Databases:

Databases consisting of data derived experimentally such as

nucleotide sequences and three dimensional structures are known as
primary databases.

Secondary Databases:

Those data that are derived from the analysis or treatment of primary
data such as secondary structures, hydrophobicity plots, and domain
are stored in secondary databases

Online Database Links

Prokaryotic Genomes

MAGPIE: Multipurpose Automated Genome Project

Investigation Environment
Microbial Genome Databases (MBGD)
Comparative Genome Analysis in P.Brok Laboratory
TIGR:The Comprehensive Microbial Resource
U.S Dept. of Energy Joint Genome Initiative

Genomic Databases of Model Organisms

Arbidopsis ThalianaGenome DIsplayer

A.Thaliana Information Resource TAIR
Caenorhabditis Elegans (worm)Database
C.Elegans Chromosomes
C.Elagans Genome Project
C.Elegans Proteome Database
Dictyostelium Discoideum Genome Information
Drosophila Melanogaster Berkeley Drosophila Genome Project
D.Melanogaster Chromosomes
D.Melanogaster:Flybase,a Genomic Database
E.Coli Genome and Proteome Database(GenProtEC)
E.Coli Index
E.Coli Genome Project
Sacchhromyces cerevisiae 16 Chromosomes
S. Cerevisiae, YPD YeastProteome Database
S. Cerevisiae,(Budding Yeast)Database SGD

Genome Databases

Genome Databases at NCBI (index)

Genome Databases at NCBI (Entrez)
Genome Databases at NCBI (PMGif) Genome List in NIH
Mitochondrial DNA Database MitBASE
Mouse (Musmusculus)genome informatics
Plant Genome Project supported by the plant genome initative
of US National science Foundation
Organelle Genome Sequences(PMGif)
Organelle Genome Sequences(PIR)
Parasites Genome Database and Genome Research resources
Retroviral Genotyping and Analysis
Rice (Oryza Sativa) Genome Project

Human and Mouse Genome Comparisons

Celera Genomics
Cooperative of Human Linkage Center:Mouse-clickable Map of
Chromosome
Draft Human Genome Browser
Human Sequence Polimorphisms,Mutation and Mapping

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Human EST Project
Human Genome Resources at NCBI
Human Genome Research Sites Provided by Oak "Ridge
National Lab
Mouse Chromosomes:mouse-Clickable map
Online Inheritance in Man: Johns Hopkins University and NCBI
Whitehead Institute of Biomedical Research

Gene and Genome Relationship and Proteome Analysis

Alfresco:Visualization Tool for Genome Comparison

Allegens.org:A Comparative gene Index(catalog) derived from
EST and Predicted Genes
CGAP:Cancer Genome Anatomy Project
COG:Cluster of Orthologous group A Gene Classification
System
DOGS:Databases of Genome sizes
E-CELL A modelling and Simulation Environment for
Biochemical and Genetic Processes
FAST_PAN for automatic searches of online EST Database to
Identify new Family Members
GeneCensus Genome Comparison by Encoded Protein
Structures
GeneQuiz:An Integrated System for large Scale Biological
Sequence Analysis and Data Management
Gene and Disease:Map Location on Human Chromosomes
Genome Channel at Oak Ridge National Laboratories
GOLD: Genome Online Database
IMGT: ImMunoGeneTics Database
Specializing in Immunoglobulin,T-Cell Receptor,and Major
Histocompatibility Complex(MHC)of all Vertibrate Species
KEGG:Kyto Encyclopedia of Gene and Genomes
MIA:Molecular Information Agent
Orthologous Gene Alignment at TIGR
PEDANT: A Protein Extraction, Description and Analysis Tool
SEQUEST for Identification of Proteins Following Mass
Spectrometry
STRING:Search Tool for Recurring Instances of Neighboring
Genes
Taxonomy Browser at NCBI arranges genomes taxonomically
for sequence retrieval
UniGene Systen Gene Oriented Clusters of GeneBank
Sequence
Usefull for Gene Identification
U.S Dept. of Agriculture Research Service Reference Site for
Plant and Animal Genome

Metabolism and Regulation,Functional Genomics

2DGel Analysis of Protein: List oF Organism

AlignAce for Promoter Analysis of coordinately regulated Genes
Array Express Database at European Bioinformatics Institute for
Microarray Analysis
BRITE:Data Base of Protein-Protein interaction and Cross
Reference Links
Ecocys Elecronic Encyclopedia of Gene and Metabolismof
E.Coli
EpoDBis:A Database of Gene that Relate to Vertibrate Red
Blood Cells(Erythropoiesis)
Expression Profiler Tool for Analysis and Clustering of Gene
Expression and Sequence Data
Functional Genomics Sites
GeneCensus Genome Comparisons by Encoded Prtein
Structures
GENECLUSTER
GeneX: A CollaborativeInternet Database and Toolset for Gene
Expression Data
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MetaCus metabolic Encyclopedia
Microarray Guide
Microarray Project at NCBI
Microarray Software
Microarrays.org: A new Public source for Microarraying
information,tools,and Protocols
SMART: for the Study of Genetically mobile protein Domaines
SWISS-2DPAGE:Two Dimentional Polyacrylamide Gel
Electrophoresis Database
TIGR: Annotation and Gene Indexing Resources,including
anlysis of the transcribed sequence represented in the Public
EST
Databases
WIT:Interactive Metabolic Reconstructionon the Web
Yeast Transcriptome
Yeast Genome on a Chip

Gene Nomenclature, Functional Characterization,and Genome

Database Development

A Thaliana Nomenclature
GAIA: Genome Annotation and Information Analysis
GeneQuiz: An Integrated System for Large-Scale Biological
Sequence Analysis and Data Management
GFF (Gene Finding Features):Specificationfor Describing Gene
and other features of Genome
GO (Gene Ontology) controlled vocabulary
K2 System for support of distributed Heterogeneous Database
and Information Resource Integration
Kleisli Project: A Tool for Broad-Scale Integration of Databanks
across the Interner
MAGPIE: Multipurpose Automated Genome Project
Investigation Environment
MAGPIE: Multipurpose Automated Genome Project
Investigation Environment(tools)
Mendel Plant Gene NomenClature Database
RefSeq and LocusLink:A Curated set of Reference Sequence
with map Locations,a Foundation for Functional Annotation of
the
Human Genome
TAMBIS: A Conceptual model of Molecular Biology
andBioinformatics and Methods for Querying the Model

RNA Databases

Compilation of tRNA sequences and sequence of tRNA genes

Small RNA databases,Baylor College of Medicine
RDP [ the Ribosomal Database Project ]
Structure of small ribosomal subunit RNA
Structure of large ribosomal subunit RNA
RNA modification database
16SMDB and 23SMDB [16S and 23S RNA mutation database ]
5S Ribosomal RNA dtabank
5S rRNA database
Comparative RNA
GenLang linguistic sequence analyzer
Gobase for mitochondrial sequences
Intron analysis-Saccharomyces cerevisiae
tRNA genes, higher plant mitochondria
MFOLD minimus energy RNA configuration
Nuclic acid database and structure resource
Pseudobase-pseudoknot database
Ribonuclease P database
Ribosomal RNA mutation database
Ribo Web Project-3D models of E-coli 30S ribosomal subunits
and 16S rRNA
RNA aptamer sequence database
RNA editing websites, UCLA
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RNA editing, uridine insertion/deletion
RNA modification database
RNA secondary structures, Group I introns, 16SrRNA. 23SrRNA
RNA structure database
RNAworld at IMB Jena
rRNA- Database of ribosomal subunit sequences
Signal recognition particle database
Small RNA database
snoRNA database for S.cerevisiae
tmRNA database
tmRNA website
tRNAscan-SE search server
tRNA and tRNA gene sequence
uRNA database
Vienna RNA package for RNA secondary structure prediction
and comparison
Viroid and viroid-like RNA sequences

Mutation Databases

HAMSTeRS [ haemohilia A mutation databases ]and factor Vlll

mutation databases]
Haemophilia B [ point mutation and short additions and
deletions ]
Human p53, hprt and lacZ genes and mutations
PAH mutation analysis [ disease-producins human PAH loci ]
16SMDB and 23SMDB [16S and 23S RNA mutation database ]
Androgen receptor gene mutaion database
p53 mutation in human tumors and cell lines

Immunogenic and Receptor Databases

IMGT [ immunogenetics databases ]

Glucocorticoid receptor resource
Thyroid hormone receptor resources

Protein Structural Databases

PDB: Protein Data Bank

Molecular Modelling Database(MMDB)
Structural classification of protein at Cambridge
University(SCOP)
Biomolecular structure and modelling group at the University
college ,London
Europian Bioinformatics institute Hinxton,Cambridge
Swiss Institute of Bioinformatics

Database of Patterns and Sequence of Protein Families

D-Ali
3D-PSSM
BLOCKS
COGS: Clusters of Orthologous Group Database and Search
site
DIP:Database of Interacting Protein
eMOTIF
HOMSTRAD
HSSP:Sequence similar to proteins of known structure
INTERPRO: Integrated resource of protein domain and
functional sites
LPFC
Pfam
PIR
PRINTS
PROCLASS
Prosite

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