title: Pattern discovery for microsatellite genome analysis.
abstract: Microsatellite loci comprise an important part of eukaryotic genomes. Their applications in biology as genetic markers are related to numerous fields ranging from paternity analyses to construction of genetic maps and linkage to human disease. Existing software solutions which offer pattern discovery algorithms for the correct identification and downstream analysis of microsatellites are scarce and are proving to be inefficient to analyze large, exponentially increasing, sequenced genomes. Moreover, such analyses can be very difficult for bioinformatically inexperienced biologists. In this paper we present Microsatellite Genome Analysis (MiGA) software for the detection of all microsatellite loci in genomic data through a user friendly interface. The algorithm searches exhaustively and rapidly for most microsatellites. Contrary to other applications, MiGA takes into consideration the following three most important aspects: the efficiency of the algorithm, the usability of the software and the plethora of offered summary statistics. All of the above, help biologists to obtain basic quantitative and qualitative information regarding the presence of microsatellites in genomic data as well as downstream processes, such as selection of specific microsatellite loci for primer design and comparative genome analysis.
authors: Department of Computer Science, Aristotle University of Thessaloniki, 54124, Greece. Electronic address: ikavak@csd.auth.gr.
authors: Ioannis
authors: I
authors: Kavakiotis
authors: Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Greece.
authors: Alexandros
authors: A
authors: Triantafyllidis
authors: Department of Computer Science, Aristotle University of Thessaloniki, 54124, Greece.
authors: Patroklos
authors: P
authors: Samaras
authors: Department of Computer Science, Aristotle University of Thessaloniki, 54124, Greece.
authors: Antonios
authors: A
authors: Voulgaridis
authors: Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Greece.
authors: Nikoletta
authors: N
authors: Karaiskou
authors: Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Greece.
authors: Evangelos
authors: E
authors: Konstantinidis
authors: Department of Computer Science, Aristotle University of Thessaloniki, 54124, Greece.
authors: Ioannis
authors: I
authors: Vlahavas
mesh_terms: D030561:Databases, Nucleic Acid; D015894:Genome, Human / Q000502:physiology*; D006801:Humans; D018895:Microsatellite Repeats; D010363:Pattern Recognition, Automated / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: Bioinformatics software; Genome analysis; Microsatellites; Mining methods; Pattern discovery; Simple sequence repeats