Next Article in Journal
RNA Splicing Factors and RNA-Directed DNA Methylation
Previous Article in Journal
Automated Sample Preparation Platform for Mass Spectrometry-Based Plasma Proteomics and Biomarker Discovery
Previous Article in Special Issue
R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Article Menu

Export Article

Open AccessArticle
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)
View Full-Text   |   Download PDF [664 KB, uploaded 11 March 2014]   |  


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).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

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

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Biology EISSN 2079-7737 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top