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

Rubino F, Attimonelli M - BMC Bioinformatics (2009)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology E, Quagliariello - Bari, 70126, Italy. rubino.francesco@gmail.com

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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.

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Regular expression describing the MA of the Meloidogyne genus 18s group 07 available in PPNEMA.
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Figure 2: Regular expression describing the MA of the Meloidogyne genus 18s group 07 available in PPNEMA.

Mentions: When phytoparasite nematologists produce a new sequence, they need to classify it as regards both function and species. The application of REB through the "characterize your sequence" option available in PPNEMA is of great help in this case. The algorithm searches for a perfect match between the query sequence and PPNEMA multi-alignments. An example is shown in Figure 1, in which the matching region is highlighted; Figure 2 reports the RegExp pattern describing the matching MA.


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

Rubino F, Attimonelli M - BMC Bioinformatics (2009)

Regular expression describing the MA of the Meloidogyne genus 18s group 07 available in PPNEMA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697652&req=5

Figure 2: Regular expression describing the MA of the Meloidogyne genus 18s group 07 available in PPNEMA.
Mentions: When phytoparasite nematologists produce a new sequence, they need to classify it as regards both function and species. The application of REB through the "characterize your sequence" option available in PPNEMA is of great help in this case. The algorithm searches for a perfect match between the query sequence and PPNEMA multi-alignments. An example is shown in Figure 1, in which the matching region is highlighted; Figure 2 reports the RegExp pattern describing the matching MA.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology E, Quagliariello - Bari, 70126, Italy. rubino.francesco@gmail.com

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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.

Show MeSH