GTOP:What is GTOP ?

What is GTOP?

Last update : Sep 16 2008
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  1. What is GTOP ?

    GTOP is a database consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures.

    We use the following methods:

    Please take a look at the Organism section for a list of the species.

  2. Results of analysis

    For each gene, a screen display like the one below is presented. This is the figure of the Homo Sapiens ENSG00000196876.3 gene ( view the ENSG00000196876.3 page)

  3. Viewing predicted 3D structure

    If you click the PDB code, 1b3qA in the above example, you can view a structure alignment (view the 1b3qA alignment). To display the corresponding 3D structure, you have three choices: images, Chime plug-in, and rasmol. To view predicted 3Dstructures using Chime plug-in and rasmol, you must configure your own computer. The procedures are described in the page How to view 3D structure.

    When information on the exon-intron structures is available, marks in different colors are displayed to distinguish exons.


    When the status of [Exon Display] is [ON], the three-dimensional structure is displayed in the same color scheme as in the alignment screen.

  4. Master file

    In the GTOP database, analytical results are stored as master-files. The information of the master file is shown after the graphical representation. Please refer to What is master file ? for the details.

  5. Search engines

    Full text search against the master file is available. In the ORGANISM box, you can select a kingdom or viruses, as well as a particular organism. As many as three query words can be specified. Entries with all of the specified words are searched. Wildcards can be used to conduct search with partial words.


    The following four kinds of search can also be conducted:

    1. Advanced Keyword Search
      You can specify the organism(s) in which to carry out this search.

    2. Family Ranking Search
      You can get a list of frequently appearing families in each organism, in terms of SCOP, Pfam, Prosite, or Membrane.

    3. Sequence homology search
      You can enter an amino acid sequence to search all the protein sequences in GTOP for it`s homologs.

    4. Sequence Text Search
      You can enter an amino acid sequence to search all the protein sequences in GTOP for those containing the exact sequence.

  6. Summary page

    From the summary page of various statistical data of whole genomes you can obtain a list of all the proteins, that of proteins whose structures are predicted by PSI-BLAST, and those of the numbers of predicted structures belonging to SCOP , Pfam and ProSite families. Links to corresponding genes can be found.

  7. Miscellaneous

Please send your inquiries or comments on GTOP to

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