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In Silico Biology 5, 0040 (2005); ©2005, Bioinformation Systems e.V.  

FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs

Kumar Gaurav, Nitin Gupta1,2 and Ramanathan Sowdhamini*

National Centre for Biological Sciences, UAS-GKVK campus, Bellary Road, Bangalore 560 065, India
1 Department of Computer Science, Indian Institute of Technoloy, Kanpur, India
2 Present address: University of California,San Diego, USA

* Corresponding author; E-mail:

Edited by E. Wingender; received June 24, 2005; revised and accepted August 25, 2005; published October 22, 2005


We present an algorithm to detect remote homology, which arises through circular permutation and discontinuous domains. It is also helpful in detecting small domain proteins that are characterized by few conserved residues. The input to the algorithm is a set of multiply aligned protein sequence profiles. This method, coded as FASSM, examines the sequence conservation and positions of protein family signatures or motifs for the annotation of protein sequences and to facilitate the analysis of their domains. The overall coverage of FASSM is 93% in comparison to other validation tools like HMM and IMPALA. The method is especially useful for difficult relationships such as discontinuous domains during whole-genome surveys and is demonstrated to perform accurate family associations at sequence identities as low as 15%.

Availability: Available upon request from the authors.

Keywords: function annotation, genome databases, protein subfamily, superfamily, function prediction