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ProtoNet News

ProtoNet v6.1, November 2012

What is new:

Database extension

  • Sequences: ProtoNet 6.1 supports Swissprot and TrEMBL DBs with over 9 million proteins from UniProt 15.4.
  • Clustering: A new efficient algorithm was developed and implemented to cluster all pairwise BLAST E-score based on UniRef50.
  • External Sources: Each proteins and clusters are linked to the annotations and features originated from Gene3D, Superfamily, UniProt, ENZYME, InterPro, NCBI Taxonomy, SCOP, GO and more.

Protein Card

  • Searching mode:Proteins are searched by any keyword from major external sources and their combinations.
  • Protein features:Proteins are associated with graphic domain representation according to the individual resources from InterPro and the detailed features according to UniProtKB.

Cluster Page

  • Cluster Definition: Each cluster is associated with a major family name determined automatically according to integration of external resources. Clusters can be searched by their dominant family names.
  • Cluster Sub-tree: Each cluster is presented as a sub-tree with its neighboring clusters. Only significant merges are presented.
  • Cluster Statistics: At any level of the tree hierarchy, clusters are assigned with statistical measures that indicate their level of purity.
  • Cluster Taxonomical genome view:At any level of the tree hierarchy,clusters can be viewed by pre selected genome and genomes combinations.
  • PANDORA analysis: PANDORA analysis: For any cluster, a view by PANDORA is provided allowing integrating all annotation associated with the proteins in the cluster (
  • Cluster Analysis: Each cluster can be viewed by ?cluster-browser? option that provides the BLAST results for all protein pairs within the cluster.

Advanced Mode

  • Clustering merging rules: ProtoNet will support few modes of clustering and the tree based on a subset of sequences such has UniRef50 and complete proteomes.
  • Clustering sub-tree: A user selection of the tree condensation and resolution.

Site Map

  • A detailed tour is presented to allow a new user to become acquainted with many of the ProtoNet options and capabilities.


Related publication

  • Rappoport, N., Linial, N., and Linial, M. (2013). ProtoNet: charting the expanding universe of protein sequences. Nature biotechnology, 31(4), 290-292.
  • Loewenstein, Y., and Linial, M. (2008). Connect the dots: exposing hidden protein family connections from the entire sequence tree. Bioinformatics 24, i193-199.
  • Loewenstein, Y., Portugaly, E., Fromer, M., and Linial, M. (2008). Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics 24, i41-49.
  • Portugaly, E., Linial, N., and Linial, M. (2007). EVEREST: a collection of evolutionary conserved protein domains. Nucleic Acids Res 35, D241-246.
  • Sasson, O., Kaplan, N., and Linial, M. (2006). Functional annotation prediction: all for one and one for all. Protein Sci 15, 1557-1562.
  • Kaplan, N., Vaaknin, A., and Linial, M. (2003). PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res 31, 5617-5626.