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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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