THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES

Year 2017, Volume: 35 Issue: 4, 763 - 770, 01.12.2017

Nehir Özdemir Özgentürk Gamze Turan Nur Hatice Aydın Salih Ulu Zehra Ömeroğlu Ulu

Abstract

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.

Keywords

Bioinformatics, EST, SSR, Olive ( Olea europaea L.).

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