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C. elegans DB

WormBase -SteinLab/CSHL

ACeDB

NEMBASE -- A database resource currently being developed at B'NG to provide a simple easy-to-use access point to the publically available nematode sequence and functional data as part of our Expressed Sequence Tag (EST) sequencing initiative [john.parkinson@ed.ac.uk]

AmphibiaWeb
Anticancer agents
ATCC
Alt-Splicing Catalog
Apoptosis
BioMagResBank
A Repository for Data from NMR Spectroscopy on
Proteins, Peptides, and Nucleic Acids (Department of Biochemistry University of Wisconsin-Madison).
BBID-Biological Biochemical Image Database -
a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics (Kevin G. Becker, NIA, NIH).
BLOCKS - Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
Brain
  • Braininfo - Provides NeuroNames, Template Atlas of the Primate Brain, & NeuroMaps ( U. of Washington, U.S.)
  • Image database - (National Functional Magnetic Resonance Imaging (fMRI) Data Center)
Calcium binding proteins database (EF-hand). Provides tools, databases, and links on all aspects of calcium binding proteins (Melanie Nelson/Walter Chazinlab; The Scripps Research Institute; Structural Biology Program at Vanderbilt U).
Cancer DB

Cancer

CarbBank - Complex Carbohydrate Structure Database (Scott Doubet).

C. elegans

Chemoreception
CGC C. elegans Genetic Center

Chemistry

Chemistry db

Computational Chem. List

Chromosome 12 - Human/Sanger
Codon Usage (all organism)
COGs Phylogenetic classification of proteins encoded in complete genomes

Combinatorial Chemistry

Biotech Applied

Combichem net

Computational Bioscience

Conserved Diseases

Genes

Motifs

CONTIGS

Human Mouse Wash. U.

Genome Channel (ORNL)

COS
CRISP
Crystallization db
Cultured Cell Bank
CYP450
Cytokine online pathfinder encyclopedia (COPPE; Horst Ibelgaufts at the Laboratory of Molecular Biology, Gene Center, University of Munich; LMU).
Cytomer
D. discoideum

 

Disease
  • GeneDis Human Genetic Diseases Compare your sequence to a sequence present in GeneDis with Pairwise Alignment; compare your protein or DNA sequence to all protein or DNA sequences in GeneDis, with FastA; compare your protein sequence to DNA sequences present in GeneDis, with TFastA (Bioinformatics Unit Faculty of Life Science Tel-Aviv University
    Israel).
  • Disease & Orphan Drugs: (OrphaNet, Infobiogen, Cedex, France)
DNA-Binding Proteins

DNA Microarrays

DNA Miropeats - discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically (jparsons, MRC, UK).

DNA Replication (Mark Griep; Center for Biotechnology, U. Nebraska-Lincoln).

Drugs

Elemental Data Index

EMBOSS suite of applications - containing around 100 programs; these are just some of the areas covered:

  • Sequence alignment
  • Rapid database searching with sequence patterns
  • Protein motif identification, including domain analysis
  • EST analysis
  • Nucleotide sequence pattern analysis, for example to identify CpG islands.
  • Simple and species-specific repeat identification
  • Codon usage analysis for small genomes
  • Rapid identification of sequence patterns in large scale sequence sets.
  • Presentation tools for publication
Enzyme - a nomenclature database, including searches by various methods and links to related databases (HMS Beagle 5/11/00).
e-PCR (all organism)
EST
  • est_genome - a software tool to aid the prediction of genes by sequence homology. The program will align a set of spliced nucleotide sequences (ESTs cDNAs or mRNAs) to an unspliced genomic DNA sequence, inserting introns of arbitrary length when needed. In addition, where feasible introns start and stop at the splice consensus dinucleotides GT and AG (HGMP,MRC,UK)
Ethanol db
FingerPRINTScan

FishBase

Flavor & Fragrance
FLY
Funded Research
Fungus2000 db - British Microbiological Society
GABA Agent
GDB
Gene Exp & Function (C. elegans)

Gene-finding software Site

Read about it

  • ACEMBLY - A graphic interactive program to support shotgun and directed sequencing projects (Danielle & Jean Thierry-Mieg and Ulrich Sauvage, CNRS-CRBM, Montpellier, France).

  • BLOCKS

  • est_genome - a software tool to aid the prediction of genes by sequence homology. (HGMP,MRC,UK)

  • FGNEH

  • Fgenes+

  • GENEID

  • GENIE

  • GENSCAN

  • GeneMarkHMM

  • GRAIL

  • GlimmerM

  • GeneBuilder

  • Genemark (The Borodovsky Group
    School of Biology,
    Georgia Institute of Technology).

  • HMMGene

  • MORGAN - an integrated system for finding genes in vertebrate DNA sequences. MORGAN uses a variety of techniques to accomplish this task, the most distinctive of which is a decision tree classifier (S. Salzberg, A. Delcher, K. Fasman, and J. Henderson. A Decision Tree System for Finding Genes in DNA).

  • SIM4 - addresses the problem of efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene, allowing for introns in the genomic sequence (taking into account consensus splice signals) and a relatively small number of sequencing errors (Florea et al. 1998, Genome Res. 1998 8:967-74).

  • VEIL - the Viterbi Exon-Intron Locator uses a custom- designed hidden Markov model (HMM) to find genes in eukaryotic DNA (John Henderson, Steven Salzberg, and Ken Fasman at Johns Hopkins University).

  • Wise2/Genewise

Gene Annotation Tools

Gene Annotation sites

Gene Annotation Tools

  • Bioxml

  • BostonAnnotator - Simultaneous analysis of genomic sequence using BLASTx and BLASTn homology searches and the GENSCAN protein prediction program. The results are displayed graphically in a manner such that alignments for all searches appear in the same window, allowing the rapid assessment of which positives correspond to real genes (Beier and Yang, Harvard U., U.S.)

  • GFF

  • GFFTOOLS

  • Publications

Gene Resume

  • euGenes (Eukaryotic Genes db; Indiana, USA).

  • Entrez All Genomes (NCBI).

  • GeneCards (human + disease; Weizmann Institute, Israel).

  • Gold (Integrated Genomics Inc., Chicago, IL, USA). Genomic links (Gold).

  • KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).

  • Stress Genes & their protein products Network - European Science Foundation (Maresca, Italy; Mayer, U.K.).

  • TIGR (Institute for Genome Research, Rockville, MD, USA).

Genes
Gene Trap Insertions

Genetic code

Genetics
Genetics & Genomics

Gene Knockout

Genome Shotgun Reads
Genomic CONTIGS
GOLD - (Genomes On Line db) providing access to all genome db, indices, etc.
Glycolysis
G Protein Coupled Receptors (GPRC)
Stem Cell Database
HGBASE - HGBASE Curated and annotated sequence variations in the human genome are presented with details of how they are physically and functionally related to the closest neighboring gene. Records include SNPs, Indels, simple tandem repeats, and other sequence alternatives [Karolinska Institute (Sweden), European Bioinformatics Institute (UK), European Molecular Biology Laboratory (Germany), & Interactiva GmbH (Germany) hosting a parallel HGBASE Web site with genotyping products (Science May 2000).
Histone Sequence
HIV -
  • HIV sequence DB - Los Alamos, NM.
  • EpiVax - Screen any of 40,000 published protein sequences of the chameleon-like HIV-1 virus, including tens of thousands of sequences from HIV-1 strains afflicting African and Indian populations, for putative epitopes (EpiVax & Brown U., Rhode Island, U.S.)
HMMER 2.1.1
Profile hidden Markov models for biological sequence analysis - can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis (Wash U., Stl.)
HMMFS - search for repeats (S. Eddy & R. Durbin; Institut Pasteur, france).

Homeobox genes

HotMolecbase targets for drugs

Human - Mouse

Hybridoma Bank

 

Immunology
InterPro protein domains & functional sites

Intron Database

Ion Channels:

KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).
LocusLink? - curated sequences, description & alphabetic lists of genetic loci, search function, , related links, etc. (NCBI, USA).
Metabolic & regulatory pathways - KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).

Microarrays

Microbial db

Model Organisms

Projects & Databases

Molecular Probe human/ viral (MPDB)

Monosaccharides
Mouse
Muscle
Mutation db
Nematodes
Neurospora
NEXTDB - nematode expression pattern database
NMR
  • BioMagResBank
    A Repository for Data from NMR Spectroscopy on
    Proteins, Peptides, and Nucleic Acids (Department of Biochemistry University of Wisconsin-Madison).
Nuclear Receptors
Organelle Genome
  • GOBASE - taxonomically broad, organizes and integrates diverse data related to organelles & especially to mitochondria.

Oligonucleotides human/viral

(MPDB)

ORNL

OWL -nonredundant protein

sequence with links to other db

Pathways
  • Dicussion of Complex Biological Pathways
  • BBID-Biological Biochemical Image Database -
    a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics (Kevin G. Becker, NIA, NIH).
  • BIND - Biomolecular Interaction Network Database
  • Boehringer Mannheim Pathways Chart
  • BRITE - Cell Cycle & Development
  • CSNDB - Cell Signaling Networks Database of signaling pathways of human cells constructed on ACEDB and inference engine CLIPS , and has a linkage to TRANSFAC. [Takako Takai-Igarashi and Tsuguchika Kaminuma; National Institute of Health Sciences (NIHS)].
  • DIP - Database of Interacting Proteins
  • EcoCyc - Encyclopedia of E. coli Genes and Metabolism
  • Interactive Fly
  • KEGG: Kyoto Encyclopedia of Genes and Genomes - providing metabolic & regulatory pathways of unicellular and mutlicellular organisms (Institute for Chemical Research, Kyoto U.).
  • Kohn Molecular Interaction Maps
  • Nuclear Receptor Resources
  • PathWays+ Metabolic Database
    (Raymond S. Ochs
    Veejay K. Sani;
    St. John's University).
  • STKE - Signal Transduction Knowledge Environment.
  • STKE db & model organisms

  • WIT - a www-based system to supporting curation of function assignments made to genes and the development of metabolic models (Argonne Computational Biology Group).

Pedant - a protein extraction, description, and analysis tool. Supplies computational analysis of sequences, genome analysis and annotation, and information on unfinished sequences (HMS Beagle; 5/12/00).
Phenology Model
Physics
PhysioNet - physiologic signals and related open-source software
Primase

PRINTS

PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database Version 2.0 (U. of Leeds).
Protein MSPcrunch: A BLAST post-processing filter - searches SWIR (non-redundant data bases of SwisProt, SP-TREMBL, & WormPep)(Sonnhammer &, Durbin).

Protein Data Bank - single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

Protein Kinases

Proteome Analysis
PSORT - Protein Cellular localization sites in Cells
Puffer Fish
Rat Databases
Rat Genomic Tools
Repeatmasker

 

Retroviruses
RNA (Scottish RNA Club; MRC, UK).
  • Non-coding
  • Ribosomal Database Project (RDP) provides ribosome related data services including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
  • RNA Editing - Larry Simpson (UCLA, USA).
  • RNA Modification - Crain & McCloskey (Chem. & Biochem, U. Utah, USA).
  • RNA World - (IMB Jena, Germany).
  • rRNA - Biochemistry: Molecular Biology (U. Antwerp (UIA), Belgium).
  • Small RNA - a searchable database (K. Perumal, J. Gu, Y. Chen, R. Reddy;
    Baylor College of Medicine).
  • Small RNA in model Organisms (K. Perumal, J. Gu, Y. Chen, R. Reddy;
    Baylor College of Medicine).
  • snoRNA - Sean Eddy Lab (Genetics, Wash. U. St. Louis, MO, USA).
  • tRNA - Stephan Brock, Laboratorium für Biochemie (Bayreuth, Germany).
  • TRNAscan_SE - Search for tRNA (S. Eddy, Wash. U., StL.).
RNAi
Sanger Center Sitemap
SCOP Structural Classification of Proteins

SNPs

Sequencing Centers

Signal Transduction - CSNDB
Signal Transduction Pathways
S/MAR transaction

SRS6-EBI A unified db

Sterols
Stress Genes & their protein products Network - European Science Foundation (Maresca, Italy; Mayer, U.K.)
STS electronic PCR
SWISS-PROT nonredundant,
annotated protein sequences

TAB: Human/viral

oligonucleotides up to

100-bp (MPDB)

Taxonomy Browser
TCA Cycle

Transcription Factor

Transgenic Mutation db
TrEMBL
Computer-annotated supplement to SWISS-PROT
VAST - Searches for similarity between proteins

Vectors

WormBase
Worm db links
Xenopus
Yeast
Zebrafish