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Biology 2014, 3(1), 220-242; doi:10.3390/biology3010220

Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes

* ,
Department of Computer Science, University of Leipzig, Postfach 100920, Leipzig D-04009, Germany
* Author to whom correspondence should be addressed.
Received: 31 October 2013 / Revised: 15 February 2014 / Accepted: 18 February 2014 / Published: 11 March 2014
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
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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.
Keywords: suffix tree; conserved sequence; mitochondrial genomes; annotation suffix tree; conserved sequence; mitochondrial genomes; annotation
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Moritz, R.L.V.; Bernt, M.; Middendorf, M. Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes. Biology 2014, 3, 220-242.

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