Sequence motifs using InterProScan


InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

The InterProScan script (obtained from ) is used to identify motifs from the following sources:

  • PROSITE patterns
  • PROSITE profiles
  • ProDom
  • Smart HHMs
  • Pfam HHMs
  • PIR SuperFamily

where "HHMs" are methods that employ Hidden Markov Models.

For full descriptions of the databases, see

InterPro Databases


The link below explains the results shown by ProFunc for motifs matched by InterProScan.
Key to results


  1. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJA, Vaughan R, Zdobnov EM (2003). The InterPro Database, 2003 brings increased coverage and new features. Nucl. Acids Res., 31, 315-318.
  2. Zdobnov EM and Apweiler R (2001). InterProScan: an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.