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Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes
Jacques Nicolas1, Patrick Durand, Grégory Ranchy
1IRISA-INRIA, Campus de Beaulieu, 35402 Rennes cedex, France. stan@irisa.fr
Bioinformatics (Oxford, England)
|October 15, 2005
Summary
We created STAN (suffix-tree analyser), a tool for searching complex DNA and protein patterns in entire chromosomes. This method efficiently handles large, unassembled genomic sequences using suffix-tree analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Analyzing large DNA sequences for specific patterns is crucial in genomics.
- Existing tools may struggle with complex pattern descriptions and large datasets.
Purpose of the Study:
- To develop a novel computational tool for efficient pattern searching in genomic sequences.
- To enable the detection of complex patterns including ambiguities, repeats, and gaps.
Main Methods:
- Developed STAN (suffix-tree analyser), a tool utilizing suffix-tree data structures.
- Implemented a string variable grammar-like formalism for pattern description.
- Reduced pattern matching to multipart matching on the suffix tree.
Main Results:
- STAN can search for both nucleotidic and peptidic patterns.
- The tool effectively handles complex pattern definitions (ambiguities, insertions/deletions, gaps, repeats, palindromes).
- STAN demonstrates capability in processing large, potentially unassembled DNA sequences.
Conclusions:
- STAN provides an efficient method for searching complex sequence patterns within entire chromosomes.
- The tool is suitable for analyzing large-scale genomic data, including unassembled sequences.
- STAN advances the capabilities of pattern analysis in bioinformatics.
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