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

Abstract

Summary: 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. © The Author 2005. Published by Oxford University Press. All rights reserved.