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

Jacques Nicolas | Zendy; Patrick Durand | Zendy; Grégory Ranchy | Zendy; Sébastien Tempel | Zendy; Anne-Sophie Valin | Zendy

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

Author(s) -

Jacques Nicolas,

Patrick Durand,

Grégory Ranchy,

Sébastien Tempel,

Anne-Sophie Valin

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti710

Subject(s) - suffix tree , computer science , suffix , palindrome , string (physics) , analyser , string searching algorithm , trie , tree (set theory) , grammar , pattern matching , data structure , theoretical computer science , artificial intelligence , programming language , biology , mathematics , combinatorics , genetics , physics , philosophy , linguistics , optics , mathematical physics , gene , crispr

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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