Databases - Genomic

Human Genome Database

• Celera's draft human & Drosophila genomes
• Draft Human Genome @ NCBI
• Draft Human Genome @ UCSC
• Ensembl - automatic annotation of Eukaryotic genes
• GDB - Genome Database
• GeneCards - database of human genes, proteins and related diseases
• Mammalian Gene Collection - offers full length sequences and DNA clones for human and mouse
• STACK - Sequence Tag Alignment and Consensus Knowledgebase
• URI Honors Colloquium - Genetic Technology in the new millennium

International Nucleotide Sequence Databases

• DDBJ - DNA Data Bank of Japan
• EBI - European Bioinformatics Institute
• NCBI - National Center for Biotechnology Information

Other Organism

• Berkeley Drosophila Genome Project
• DictyBase - Dictyostelium discoideum
• EcoGene - E. coli
• FlyBase
• Fruit Fly
• GOLD - Genomes OnLine Database, information on complete and ongoing genome projects
• HIV sequence database
• Mouse
• Mouse Genome Informatics
• Rat
• Saccharomyces Genome Database
• The Arabidopsis Information Resource
• The Proteome Databases - yeast, worm, & human, good annotation
• TIGR Comprehensive Microbial Resource
• TIGR Microbial Database
• WormBase - C. elegans
• Zebra Fish
• ZFIN - Zebrafish Information Network

Databases - Proteomics

Molecular Modeling

• CATH - protein structure classification
• DALI - networking services for comparing protein structures in 3D
• DSSP - definition of secondary structure of proteins given a set of 3D coordinates
• FSSP - food classification based on structure-structure alignment of proteins
• HSSP Database - Homology-derived Secondary Structure of Proteins
• Jpred2 - method for protein secondary structure prediction
• K2 - protein structure alignment - various food recognition and local structure prediction methods
• PDB - processing and distrubutio of 3D biological macromolecular structure data
• PredictProtein & PHD - service for sequence analysis, and structure prediction
• PSIpred (& MEMSAT & GenTHREADER) - protein structure prediction server
• RasMol / Protein Explorer - software for viewing macromolecular structure
• SCOP - Structural Classification Of Proteins
• Structure Prediction Meta-server
• SWISS-MODEL - protein modeling server
• The DALI Domain Database - structure classification of protein domains

Protein Sequence Databases

• MIPS - Munich Information centre for Protein Sequences
• PIR - Protein Information Resource
• SWISS-PROT & TrEMBL - protein sequence knowledge database and computer annotated supplement

Databases of Gene Regulation and Cell Signaling

Gene Expression dasfd

• Bodymap - human and mouse gene expression datab
• ExpressDB - database containing yeast and E. coli expression data
• HuGE - human gene expression index
• Stanford Microarray Database - database of microarray experiments

Gene Regulation

• Cister - cis-element cluster finder
• DBTSS - database of transcriptional start sites
• DCPD - Drosophila Core Promoter Database
• DPInteract - DNA protein binding sites within E. coli DNA
• EPD - eukaryotic promoter database
• Kimono - find regulatory elements in promoter sequences
• MatInspector - locate transcription factor binding sites
• PromoterInspector - prediction of promoter regions in mammalian genomic sequences
• SCPD - promoter database for Saccharomyces cerevisiae
• TRANSFAC - the transcription factor database

Signal Transduction and Cell Signalling

• Alliance for Cellular Signalling
• BIND - Biomolecular Interaction Network Database
• CSNDB - Cell Signalling Networks Database
• DIP - Database of Interacting Proteins
• KEGG - Kyoto Encyclopedia of Genes and Genomes
• PathDB - research tool for biochemistry & functional genomics
• PFBP - Protein Function and Biochemical Pathways Project
• SPAD - Signaling Pathway Database
• stke - Signal Transduction Knowledge Environment
• Transpath - information system on gene regulatory pathways

Other Resources

• A Bioinformatic Thesaurus
• Computational Biology or Bioinformatics References at UCSC

Searching and Tools - Genomics

Sequence Alignment

Sequence Similarity

• Bioccelerator @ EMBL - database searches using Smith-Waterman's algorithm
• BLAST @ NCBI - basic local alignment tool
• FASTA @ EBI - sequence similarity and homology searching using FASTA
• PSI-BLAST @ NCBI - Protein blast

Tools - Proteomics

Protein Domain Families

• Blocks - a service for biological sequence analysis
• InterPro - resoure for protein families, domains, and functional sites
• Pfam - multiple sequence alignments and hidden Markov models
• PRINTS Database - protein finger prints database
• ProDom - protein domain database
• PROSITE - database of protein families and domains
• Protein Domain Profile Analysis @ BMERC - search a library of functional diagnostics profiles with a protein sequence
• SMART - simple modular architecture research tool
• TIGRFAMs - protein families based on Hidden Markov Models