title: Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.
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.
authors.affiliation: IRISA-INRIA, Campus de Beaulieu, 35402 Rennes cedex, France. stan@irisa.fr
authors.forename: Jacques
authors.initials: J
authors.lastname: Nicolas
authors.forename: Patrick
authors.initials: P
authors.lastname: Durand
authors.forename: Grégory
authors.initials: G
authors.lastname: Ranchy
authors.forename: Sébastien
authors.initials: S
authors.lastname: Tempel
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Valin
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D023281:Genomics / Q000706:statistics & numerical data*; D010363:Pattern Recognition, Automated; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant