Genome Analysis

  • SALSA DNA and Protein Sequence Database Search against complete genomes @Norway

  • COG Clusters of Orthologous Groups @ NCBI

Multi-Service Servers

  • Part of the Swiss Institute of Bioinformatics

  • IDEAS Integrated Database and Extended Analysis System for Nucleic Acids and Proteins

Homology Search Engines

  • BLAST search page @ GenomeNet, Kyoto, Japan


  • BOXSHADE 3.21 Pretty Printing and Shading of Multiple-Alignment files

  • DIALIGN 2 especially suited to detect local similarities among distantly related sequences

  • ALIGN Compendium of Protein Sequence Alignments

  • CINEMA Colour INteractive Editor for Multiple Alignments


Motifs and Searches

  • MOTIF Searching Protein Sequence Motifs

  • PRINTS Protein Motif Fingerprint Database


  • Paircoils predict the location of coiled-coil regions

  • PROSITE Dictionary of protein sites and patterns

Phylogenetic Analysis

  • NJplot for parsimony, distance or maximum likelihood trees

  • PHYLIP a package of programs for inferring phylogenies

  • PUZZLE Tree reconstruction for sequences by quartet puzzling and maximum likelihood


  • SCOP Structural Classification of Proteins

  • FSSP - Fold classification based on Structure-Structure alignment of Proteins

  • NNPREDICT Protein Secondary Structure Prediction



Sequence Reference and Retrieval-System

  • Entrez The NCBI WWW Entrez Browser

  • PROSITE Dictionary of protein sites and patterns

  • DBGET Integrated Database Retrieval System @ GenomeNet, Japan




  • RepeatMasker screens DNA against a library of repetitive elements and returns a masked query sequence ready for database searches

  • dbEST Database of Expressed Sequence Tags @ NCBI


  • ESSA an integrated and interactive computer tool for analyzing RNA secondary structure


  • PSORT Prediction of Protein Sorting Signals and Localization Sites in AminoAcid Sequences

  • Sequin for submitting entries to the GenBank, EMBL, or DDBJ sequence databases