ISSN: 1304-7191 | E-ISSN: 1304-7205
The detection of SSRs from olive (Olea europaea L.) EST collection by comparing 4 different bioinformatics oftwares
1Department of Molecular Biology and Genetics, Faculty of Science and Art, Yıldız Technical University, Esenler-ISTANBUL
2Department of Molecular Biology-Genetics and Biotechnology, Faculty of Science and Art, Istanbul Technical University, Sarıyer-ISTANBUL
Sigma J Eng Nat Sci 2017; 35(4): 763-770
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Bioinformatics is an interdisciplinary science that is formed by the combination of computer science and biology. Over the years, accumulating data were stored carefully, organized, incorporated, provided classification and accessed easily by bioinformatics. Experimental studies take a long time and are expensive but by means of bioinformatics these studies take a short time and are cheaper.
There are two approaches to determine SSRs (Simple Sequence Repeat/Microsatellite) in plants which are
analysis of DNA libraries and analysis of EST (Expressed Sequence Tag) collections. Like many studies these two approaches also benefit from bioinformatics. Thus SSRs, which were determined, can be used as markers
in genetic diversity studies.
In this study, to determine SSRs in olive EST collection that has 3734 EST; SSRIT, SSR Finder, WebSat and IMEx Softwares, which have web-based versions and are easily accessible and utilized, were used. SSR
motifs and positions of the EST collection have been determined by means of these four softwares. Each of the four softwares found 2, 3, 4 and 6-nucleotide SSRs. “GA” pattern repeated 6 times, is the most abundant
SSR with 324 occurrences. The advantages and disadvantages of the softwares used were determined by comparing the results.