Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.
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.
Nicolas
Jacques
J
IRISA-INRIA, Campus de Beaulieu, 35402 Rennes cedex, France. stan@irisa.fr
Durand
Patrick
P
Ranchy
Grégory
G
Tempel
Sébastien
S
Valin
Anne-Sophie
AS
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
D004251:DNA Transposable Elements; D018744:DNA, Plant