Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Research article

False occurrences of functional motifs in protein sequences highlight evolutionary constraints

Allegra Via1*, Pier Federico Gherardini1, Enrico Ferraro1, Gabriele Ausiello1, Gianpaolo Scalia Tomba2 and Manuela Helmer-Citterich1

Author Affiliations

1 Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma

2 Department of Mathematics, University of Rome Tor Vergata, Roma

For all author emails, please log on.

BMC Bioinformatics 2007, 8:68  doi:10.1186/1471-2105-8-68

Published: 1 March 2007

Abstract

Background

False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a numerical approach to investigate the random appearance of functional motifs with the aim of addressing biological questions such as: How are organisms protected from undesirable occurrences of motifs otherwise selected for their functionality? Has the random appearance of functional motifs in protein sequences been affected during evolution?

Results

Here we analyse the occurrence of functional motifs in random sequences and compare it to that observed in biological proteomes; the behaviour of random motifs is also studied. Most motifs exhibit a number of false positives significantly similar to the number of times they appear in randomized proteomes (=expected number of false positives). Interestingly, about 3% of the analysed motifs show a different kind of behaviour and appear in biological proteomes less than they do in random sequences. In some of these cases, a mechanism of evolutionary negative selection is apparent; this helps to prevent unwanted functionalities which could interfere with cellular mechanisms.

Conclusion

Our thorough statistical and biological analysis showed that there are several mechanisms and evolutionary constraints both of which affect the appearance of functional motifs in protein sequences.