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This article is part of the supplement: European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

Open Access Proceedings

RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences

Francesco Rubino and Marcella Attimonelli*

Author Affiliations

Department of Biochemistry and Molecular Biology "E. Quagliariello" – Bari, 70126, Italy

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BMC Bioinformatics 2009, 10(Suppl 6):S5  doi:10.1186/1471-2105-10-S6-S5

Published: 16 June 2009



One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences).

However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets.

The REB algorithm workflow consists in

i. the definition of a dataset of multialignments

ii. the association of each MA to a pattern, defined by application of regular expression rules;

iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence.


An application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA.


The use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method.