Genome Analysis


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

  • COG Clusters of Orthologous Groups @ NCBI



Multi-Service Servers




  • embNet.org 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


Alignments

  • 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




Domains

  • 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







Structure




  • SCOP Structural Classification of Proteins

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



  • NNPREDICT Protein Secondary Structure Prediction




Transcription



 

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


Genes

 

DNA


  • 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
 

RNA

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

General

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



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


Links