Protein Function Score Help

The Protein Function Score (PFS) server provides for a quick evaluation of Swiss-Prot entries with particular regard to protein function. The value of PFS for a given protein is estimated by scanning the entry information for the number and quality of publications, protein descriptions and comments such as FUNCTION and CATALYTIC ACTIVITY. The resulting number between zero and three reflects the current information content of every given Swiss-Prot member, ascending with the degree of annotation.
The manual inspection of Blast search data is a laborious task with the goal to find the best hit delivering the most informative content. By including color codes to Blast search results visualizing the three different PFS levels, hits are secondarily ranked according to their knowledge contribution and therefore more easy to analyse.
Our PFS webservice provides the following utilities:

  • The retrieval of PFS for any given Swiss-Prot entry specified by an entry name, accession number or a keyword searched in the entry decription and species name.
  • A Blastp search to compare a query protein against the Swiss-Prot sequence database. Blast hits are ranked according to E-value as usual. The PFS values of the matched proteins are highlighted by color codes with red for weak annotation, yellow for a moderate and green for a well characterized entry.
    The E-value includes a link to the detailed alignment whose color codes are adjustable via the ‘Alignment Color settings’. ‘View all results’ gives all alignments.

Result lists may be sorted alphabetically or numerically by a mouse click in the column header. Accession numbers in the output tables provide a link to respective Swiss-Prot entries at www.expasy.org.