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Bioinformatics Vol. 17 no. 4 2001
Pages 338-342
© 2001 Oxford University Press

Original Paper

Limits of homology detection by pairwise sequence comparison

Rainer Spang 1,2 and Martin Vingron 1

1 Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

Received on August 7, 2000 ; revised on December 18, 2000 ; accepted on December 21, 2000

Motivation: Noise in database searches resulting from random sequence similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database search programs, but a logical consequence of the idea of homology searches. The effect can be observed in simulation experiments.

Results: We have investigated noise levels in pairwise alignment based database searches. The noise levels of 38 releases of the SwissProt database, display perfect logarithmic growth with the total length of the databases. Clustering of real biological sequences reduces noise levels, but the effect is marginal.

Contact: rainer{at}stat.duke.edu; m.vingron{at}dkfz-heidelberg.de

2 To whom correspondence should be addressed. Pressent address: Duke University, Institute of Statistics and Decision Sciences, Box 90251 Duke University, Durham, NC 27708-0251, USA.


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