FINDING A DIFFERENT LENGTH OF MICROSATELLITE REPEATS IN THE COMPLETED GENOME OF PHOENIX DACTYLIFERA CHLOROPLAST

Ezz, Mohamed; Hussein, Amal; Hemeida, Alaa; El-Feky, Fawzy

doi:10.21608/jpd.2017.41885

FINDING A DIFFERENT LENGTH OF MICROSATELLITE REPEATS IN THE COMPLETED GENOME OF PHOENIX DACTYLIFERA CHLOROPLAST

Document Type : Original Article

Authors

¹ Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), SADAT City University, Egypt.

² Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Egypt.

10.21608/jpd.2017.41885

Abstract

Variation of SSRs is mainly caused by slipped-strand mispairing and subsequent resulting errors during DNA replication, repair, and recombination. Regular expressions applied to match the repeats of DNA sequences. In this study a programmed tool was designed by Visual basic language to detect the different lengths of SSR sequences in the chloroplast completed genome of Phoenix dactylifera (Accession number, GU811709.2). The accession number GU811709.2was downloaded from Genbank of NCBI and used as an input string to search for the different lengths of repeats by using RFRE Ver. 1.0. Different lengths of repeats (Di-repeats, Tetra-repeats, Penta-repeats and hexa –repeats) were founded by the regular expression language which used by the RFRE tool. The length of the longest repeats was forty characters. Parts of the long repeats were founded in the region of expressed gene (rps3 gene). The most abundant founded motif was (AAAA) {2} and the total length of that repeat was equal to 632.
The tool was very easy to use where it had a GUI interface and accepted different combined regular expression syntax to match different patterns of repeats in the genome of Phoenix dactylifera (Accession number, GU811709.2).The founded patterns assigned to the annotated genome map of the accession numberGU811709.2. A specific Regular Expression Pattern ([agct]{20})\1 was used to find a repeated sequences with 40 characters in length in three different locations in the genome of chloroplast (8675, 78458 and 85021).
In conclusion, this study focused on the importance of characterized and identifying the types of tandem repeats in Phoenix dactylifera (cultivar, Khalas- female) chloroplast genome by using the power of regular expression language.

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