Tool list:

  • COGcollator
    COGcollator is a web server for analysis of distant relationships between homologous protein families as derived from the COG database.
    Links:
    [Previous version]
    Downloads:
    [Download all COGs profile HMMs] 4870 profile HMMs
    Associated publications:
    • Dibrova D.V., Konovalov K.A., Perekhvatov V.V., Skulachev K.V., Mulkidjanian A.Y. (2017) COGcollator: A web service for analysis of distant relationships between homologous protein families. Biology Direct 12(29). [DOI: 10.1186/s13062-017-0198-x]
  • DomainAnalyser
    This tool provides a search for protein domains represented by HMM profiles in the Pfam database and the HMM profile database we created for Clusters of Orthologic Groups (COGs). The search is carried out by the hmmscan program of the HMMer 3.3 package. The search could be performed for a set of protein sequences. During the search, overlapping domains could be filtered, and a user can alter parameters of the filtering procedure. Search results can be downloaded both graphically and in text form.
    Links:
    [Previous version]
    Associated publications: none.
  • Alnalyser
    This software is aimed to help in a daily routine work of any bioinformatician who works with multiple sequence alignments and uses them further to build phylogenetic trees. Briefly, it is a graphical interface written on Python3/Tkinter which allows to maintain multiple projects with sequence alignment and additional data for it (e.g. hits of profile HMMs from Pfam or COG databases and predictions of transmembrane elements). Also it can be used to remove poorly aligned or truncated sequences in semi-automated mode. Finally, as a small cherry on a top, it has a sequence format converter supporting NCBI, Uniprot, PDB, COGcollator and other formats.
    Links:
    [GitHub]
    [User manual]
    Associated publications: none.
  • COGNAT
    COGNAT is a tool for comparative analysis of genomic neighborhoods. The web service provides general information about the genomic neighborhoods of proteins belonging to a particular COG or Pfam domain in a representative sample of 711 prokaryotic genomes, and the local version of the program allows you to analyze any arbitrary set of proteins. The local version of the program is available as source code in C ++.
    Links:
    [Desktop version on GitHub]
    [Tool web site]
    Associated publications:
    • Klimchuk O.I., Konovalov K.A., Perekhvatov V.V., Skulachev K.V., Dibrova D.V., Mulkidjanian A.Y. (2017) COGNAT: A web service for comparative analysis of genomic neighborhoods. Biology Direct 12(26). [DOI: 10.1186/s13062-017-0196-z]