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FASSM Server:

FASSM [Function Association using Sequence and Structural Motifs] is an algorithm developed to detect remote homology. The method is especially useful to detect difficult relationships across protein famlies. It has been shown that FASSM can be used to assign function to sequence belong to difficult categories such as discontinuous domains, small domains and circular-permutations in domains. FASSM is demonstrated to perform accurate family associations at sequence identities as low as 15%. FASSM is now available as a web server, which can be used for function association of protein sequences using FASSM approach that used Best Representative PSSM profiles (BRPs) derived from 3PFDB database.

FASSM Methodology:

FASSM explore the conservation of specific sequence signatures among the query sequence and target profile based on a scoring scheme supported by a neural network. FASSM Server examines the sequence conservation and positions of protein family signatures of a query sequence by searching against of a database of Best Representative PSSM profiles curated using a novel datamining method. Users can submit a query sequence and obtain annotation based on sequence signatures predicted by FASSM method.


  • K. Shameer, P. Nagarajan, K. Gaurav and R. Sowdhamini (2009) 3PFDB : A database of Best Representative PSSM Profiles (BRPs) generated using a novel data mining approach Submitted
  • K. Gaurav, N Gupta and R Sowdhamini., (2005)FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs. In Silico Biology, 5, 0040
  • R.D. Finn et. al., (2008) The Pfam protein families database Nucleic Acids Res., 36, D281-D288
  • Altschul S.F., et. al., (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402.


Prof. R. Sowdhamini [mini@ncbs.res.in]
Khader Shameer