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Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.

Bioinformatics

Pattern Recognition, Automated, Software, Base Sequence, Chromosomes, genetics, Chromosomes, Plant, Computational Biology, DNA Transposable Elements, DNA, Plant, Databases, Nucleic Acid, Genomics, statistics & numerical data, Amino Acid Sequence, Arabidopsis

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      Abstract

      We have developed STAN (suffix-tree analyser), a tool to search for nucleotidic and peptidic patterns within whole chromosomes. Pattern syntax uses a string variable grammar-like formalism which allows the description of complex patterns including ambiguities, insertions/deletions, gaps, repeats and palindromes. STAN is based on a reduction to multipart matching on a suffix-tree data structure and can handle large DNA sequences, whether assembled or not.

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      Journal
      10.1093/bioinformatics/bti710
      16223791

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