tRNA diversification among uncultured archeon clones

Mohammad Mahfuz Ali Khan Shawan; Md Ashraful Hasan; Raihana Yesmin; Tareq Hossan; Md Mozammel Hossain; Md Mahmudul Hasan; Afroza Parvin; Mahbubul Morshed; Nahiyan Mohammad Salauddin; Satya Ranjan Sarker; Md Nazibur Rahman; S M Badier Rahman

doi:10.6026/97320630014357

tRNA diversification among uncultured archeon clones

Bioinformation. 2018 Jul 31;14(7):357-360. doi: 10.6026/97320630014357. eCollection 2018.

Affiliations

¹ Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh.
² Department of Soil, Water and Environment, University of Dhaka, Bangladesh.
³ Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh.

Abstract

Whole genome sequences (DNA sequences) of four uncultured archeon clones (1B6:CR626858.1, 4B7:CR626856.1, 22i07:JQ768096.1 and 19c08:JQ768095.1) were collected from NCBI BioSample database for the construction of digital data on tRNA. tRNAscan-SE 2.0 and ENDMEMO tools were used to identify and sketch tRNA structure as well as calculate Guanine-Cytosine (GC) percentage respectively. Eight true/functional tRNAs were identified from above 4 sequences which showed cove score greater than 20% with no variable loop. The tRNAs from the uncultured archeon clones were classified as Ala, Arg, Ile, Thr, Pro and Val type tRNA with cove score ranging from 34.22%-79.03%. The range of GC content was found 42.89%-56.91%; while tRNA contributed GC content ranging from 52%-64.86% to the total GC content in these sequences. The data fabricated in this study could be very useful for studying the diversity of tRNA among prokaryotes.

Keywords: ENDMEMO GC calculating tool; GC percentage; NCBI BioSample database; Uncultured archeon clones; cove score; tRNA type; tRNAscan-SE 2.0 tool; true/functional tRNA.