FASSM

Enhanced function association in whole genome analysis using sequence and structural motifs

Kumar Gaurav, Nitin Gupta, Ramanathan Sowdhamini*

*Corresponding author for this work

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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%.

Original languageEnglish
Pages (from-to)425-438
Number of pages14
JournalIn Silico Biology
Volume5
Issue number5-6
Publication statusPublished - 2005

Keywords

  • Function annotation
  • Function prediction
  • Genome databases
  • Protein subfamily
  • Superfamily

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