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Bioinformatics Resources

Databases – Genomic

Human Genome Database

International Nucleotide Sequence Databases

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

Other Organism

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

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

  • InterPro - resoure for protein families, domains, and functional sites
  • PRINTS Database - protein finger prints database
  • PROSITE - database of protein families and domains
  • SMART - simple modular architecture research tool
  • TIGRFAMs - protein families based on Hidden Markov Models

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