Abstract
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.
Highlights
Mitochondria are organelles that fulfill vital functions in eukaryotic cells
The two marker detection methods that are introduced use the generalized suffix tree data structure that is described in Subsection 2.1
The annotation guided and probability based marker detection methods were run on the 2989 mitochondrial genome sequences contained in RefSeq and their reverse complements
Summary
Mitochondria are organelles that fulfill vital functions in eukaryotic cells. They produce adenosine triphosphate which is an important carrier of chemical energy. Mitochondria are thought to have their evolutionary origin in α-proteobacteria which have been integrated into cells by endosymbiosis. Mitochondria inherited a genome (mitogenome) from their bacterial ancestors, which has been reduced dramatically in most lineages (see [1] for an overview). The typical metazoan mitogenome is circular and usually comprises approximately 16.5 k nucleotides [2]. It comprises a nearly perfectly preserved gene content, consisting of 37 genes including
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