Documentation

The SISYPHUS alignments are accessible through three different ways: by browsing
  • alignment categories,
  • keywords, or
  • GO terms.
  • Alignment categories

    The alignments are organized into different categories based on the criteria used to group protein regions. A more detailed description of the content of each category is provided on the category page.

    Keywords

    We have developed a set of controlled vocabulary in order to catalog in more structured way various attributes of the entire protein, protein structure or structural relationship. Browsing the alignment keywords allows to obtain a group of alignments having similar property or attribute.

    GO terms

    Gene ontology terms were assigned to a given alignment if all members share similar molecular function. Therefore browsing the GO terms will retrieve only a set of alignments whose members have the same function. The full list of the alignments is accessible via the category page.

    The search engine supports queries by keywords, GO terms, pdb accession codes, protein names and taxonomy.

    SISYPHUS alignment

    The compiled information for a given alignment is available from the SISYPHUS alignment page. The alignments are visualized in Jalview alignment viewer and in HTML format with colored blocks that indicate the regions of structural similarity. The structurally equivalent positions are shown in uppercase, dissimilar regions are disregarded and shown in lower case. The letter X denotes a modified amino acid.

    Alignment relationships

    Currently, the SISYPHUS database contains two type of relationships: "is_related" and "part_of". "is_related" defines a relationship in which the criteria to group structurally related proteins into a given "child" alignment is stricter than the "parent" alignment. The "part_of" relationship identifies relation between alignments containing a compact region of protein structure and a protein fragment.

    If all alignment members share a common functional properties then a GO term is assigned to a given alignment. A link provide an access to all alignments having the same functional property.

    The information for each protein region included in the alignment is available from the alignment member page. The web site contains a detailed information for each construct in the alignment such as segment order, start and end positions of the pdb entry that define the construct, SWISS-PROT link, NCBI taxonomy and origin of the protein. The protein origin is defined by comparison to the SWISS-PROT sequence into three types: natural , variant or mutant.

    SCOP

    The relationships between SISYPHUS alignments and the nodes in the SCOP classification are complex. A given SISYPHUS alignment can correspond to many nodes and several SISYPHUS alignments can match to one SCOP node. A hyperlink provides a link to the related SCOP level(s).

    SPICE

    The regions included in the alignment can be visualized using SPICE, a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides.

    All data is retrieved from different sites on the Internet, that make their annotations available using the DAS (Distributed Annotation System) protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

    SPICE is integrated into the SISYPHUS web site. If you click on one of the links, SPICE will automatically download and start itself. Keep the application window open to load the data for a new PDB in this window.

    For more help on SPICE please proceed to the SPICE website.