2Can Support Portal - Protein Function

PPSearch example

• We submit our query sequence to PPSearch. The program accepts sequences in FASTA, GCG, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format. It does not accept raw text. You can also upload a sequence from a file.
  
  
• There are 3 parameters that you can change before you launch an application:
  
  
  • include abundant patterns: these are short patterns that are found abundantly in sequences. They match sites that are present in many sequences including amidation, phosphorylation and glycosylation sites. Matches to these short patterns give us a little insight into our query sequence but they do not provide us with information about the family to which our sequence belongs. By default this parameter is switched off.
    
    
  • view results in ascii graphics: when this is switched on, it gives us a graphical view of the positioning of the matches along our query sequence.
    
    
  • view results using a java viewer: when this is switced on, it gives us a graphical view of the positioning of the matches along our query sequence with links to the PROSITE pattern entries.
    
    
  In our example, we will first launch the application with all parameters set to 'no'
  
  
• Run the job.