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Bioinformatics Vol. 18 no. 90001 2002
Pages S38-S45
© 2002 Oxford University Press

The POPPs: clustering and searching using peptide probability profiles

Michael J. Wise

Department of Genetics, Cambridge, CB2 3EH, England

The POPPs is a suite of inter-related software tools which allow the user to discover what is statistically ‘unusual’ in the composition of an unknown protein, or to automatically cluster proteins into families based on peptide composition. Finally, the user can search for related proteins based on peptide composition. Statistically based peptide composition provides a view of proteins that is, to some extent, orthogonal to that provided by sequence. In a test study, the POPP suite is able to regroup into their families sets of approximately 100 randomised Pfam protein domains. The POPPs suite is used to explore the diverse set of late embryogenesis abundant (LEA) proteins.

Availability: Contact the author.

Contact: mw263{at}cam.ac.uk

Keywords: protein clustering; clustering algorithms; protein search; peptide composition; Pfam; late embryogenesis abundant proteins.


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