Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

Biology

Ruby L. V. Moritz¹  Matthias Bernt² 

[1]Department of Computer Science, University of Leipzig, Postfach 100920, Leipzig D-04009, Germany

关键词: suffix tree;    conserved sequence;    mitochondrial genomes;    annotation;   

DOI  :  10.3390/biology3010220

来源: mdpi

【 摘 要 】

Given a set of nucleotide sequences we consider the problem of identifying conserved substrings occurring in homologous genes in a large number of sequences. The problem is solved by identifying certain nodes in a suffix tree containing all substrings occurring in the given nucleotide sequences. Due to the large size of the targeted data set, our approach employs a truncated version of suffix trees. Two methods for this task are introduced: (1) The annotation guided marker detection method uses gene annotations which might contain a moderate number of errors; (2) The probability based marker detection method determines sequences that appear significantly more often than expected. The approach is successfully applied to the mitochondrial nucleotide sequences, and the corresponding annotations that are available in RefSeq for 2989 metazoan species. We demonstrate that the approach finds appropriate substrings.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.