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Nucleic Acids Research, 2003, Vol. 31, No. 2 683-689
© 2003 Oxford University Press

Finding weak similarities between proteins by sequence profile comparison

Anna R. Panchenko*

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA

*Tel: +1 301 435 5891; Fax: +1 301 435 7794; Email: panch{at}ncbi.nlm.nih.gov

To improve the recognition of weak similarities between proteins a method of aligning two sequence profiles is proposed. It is shown that exploring the sequence space in the vicinity of the sequence with unknown properties significantly improves the performance of sequence alignment methods. Consistent with the previous observations the recognition sensitivity and alignment accuracy obtained by a profile–profile alignment method can be as much as 30% higher compared to the sequence–profile alignment method. It is demonstrated that the choice of score function and the diversity of the test profile are very important factors for achieving the maximum performance of the method, whereas the optimum range of these parameters depends on the level of similarity to be recognized.


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