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Open Access Research article

Optimal neighborhood indexing for protein similarity search

Pierre Peterlongo1*, Laurent Noé23, Dominique Lavenier4, Van Hoa Nguyen1, Gregory Kucherov23 and Mathieu Giraud23

Author Affiliations

1 Symbiose team-project, IRISA INRIA, Rennes, France

2 LIFL, CNRS, Université Lille 1, Lille, France

3 INRIA Lille Nord-Europe, Lille, France

4 IRISA – ENS Cachan, France

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BMC Bioinformatics 2008, 9:534  doi:10.1186/1471-2105-9-534

Published: 16 December 2008



Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet.


The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website webcite.


We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.