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

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

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

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

References

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Details

Primary Language

English

Subjects

Engineering

Journal Section

Research Article

Authors

Nehir Özdemir Özgentürk This is me
0000-0003-3809-6303
Türkiye

Gamze Turan This is me
0000-0003-4563-2792
Türkiye

Nur Hatice Aydın This is me
0000-0001-9213-285X
Türkiye

Salih Ulu This is me
0000-0002-4505-0197
Türkiye

Zehra Ömeroğlu Ulu This is me
0000-0002-8884-4683
Türkiye

Publication Date

December 1, 2017

Submission Date

November 28, 2016

Acceptance Date

October 23, 2017

Published in Issue

Year 2017 Volume: 35 Number: 4

IZ

https://izlik.org/JA56LK65BL

Cite

RIS / Bibtex

APA

Özdemir Özgentürk, N., Turan, G., Aydın, N. H., Ulu, S., & Ömeroğlu Ulu, Z. (2017). THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES. Sigma Journal of Engineering and Natural Sciences, 35(4), 763-770. https://izlik.org/JA56LK65BL

AMA

1.Özdemir Özgentürk N, Turan G, Aydın NH, Ulu S, Ömeroğlu Ulu Z. THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES. SIGMA. 2017;35(4):763-770. https://izlik.org/JA56LK65BL

Chicago

Özdemir Özgentürk, Nehir, Gamze Turan, Nur Hatice Aydın, Salih Ulu, and Zehra Ömeroğlu Ulu. 2017. “THE DETECTION OF SSRs FROM OLIVE (Olea Europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES”. Sigma Journal of Engineering and Natural Sciences 35 (4): 763-70. https://izlik.org/JA56LK65BL.

EndNote

Özdemir Özgentürk N, Turan G, Aydın NH, Ulu S, Ömeroğlu Ulu Z (December 1, 2017) THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES. Sigma Journal of Engineering and Natural Sciences 35 4 763–770.

IEEE

[1]N. Özdemir Özgentürk, G. Turan, N. H. Aydın, S. Ulu, and Z. Ömeroğlu Ulu, “THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES”, SIGMA, vol. 35, no. 4, pp. 763–770, Dec. 2017, [Online]. Available: https://izlik.org/JA56LK65BL

ISNAD

Özdemir Özgentürk, Nehir - Turan, Gamze - Aydın, Nur Hatice - Ulu, Salih - Ömeroğlu Ulu, Zehra. “THE DETECTION OF SSRs FROM OLIVE (Olea Europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES”. Sigma Journal of Engineering and Natural Sciences 35/4 (December 1, 2017): 763-770. https://izlik.org/JA56LK65BL.

JAMA

1.Özdemir Özgentürk N, Turan G, Aydın NH, Ulu S, Ömeroğlu Ulu Z. THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES. SIGMA. 2017;35:763–770.

MLA

Özdemir Özgentürk, Nehir, et al. “THE DETECTION OF SSRs FROM OLIVE (Olea Europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES”. Sigma Journal of Engineering and Natural Sciences, vol. 35, no. 4, Dec. 2017, pp. 763-70, https://izlik.org/JA56LK65BL.

Vancouver

1.Nehir Özdemir Özgentürk, Gamze Turan, Nur Hatice Aydın, Salih Ulu, Zehra Ömeroğlu Ulu. THE DETECTION OF SSRs FROM OLIVE (Olea europaea L.) EST COLLECTION BY COMPARING 4 DIFFERENT BIOINFORMATICS SOFTWARES. SIGMA [Internet]. 2017 Dec. 1;35(4):763-70. Available from: https://izlik.org/JA56LK65BL