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

tRNA diversification among uncultured archeon clones

Mohammad Mahfuz Ali Khan Shawan  1 , Md Ashraful Hasan  1 , Raihana Yesmin  2 , Tareq Hossan  1 , Md Mozammel Hossain  1 , Md Mahmudul Hasan  1 , Afroza Parvin  1 , Mahbubul Morshed  1 , Nahiyan Mohammad Salauddin  1 , Satya Ranjan Sarker  3 , Md Nazibur Rahman  1 , S M Badier Rahman  1
Affiliations

tRNA diversification among uncultured archeon clones

Mohammad Mahfuz Ali Khan Shawan et al. Bioinformation. .

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.

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Figures

Figure 1
Figure 1
tRNA secondary structure and GC allocation through graphical representations in four uncultured archeon clones detected by tRNAscan-SE 2.0 and ENDMEMO GC calculator. A) 1B6:CR626858.1; B) 4B7:CR626856.1; C) 22i07:JQ768096.1 and D) 19c08:JQ768095.1
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References

    1. Maizels N, Weiner AM. Proc. Natl. Acad. Sci. 1994;91:6729. - PMC - PubMed
    1. Goodenbour JM, Pan T. Nucleic Acids Res. 2006;34:6137. - PMC - PubMed
    1. Fujishima K, et al. PLoS One. 2008;3:e1622. - PMC - PubMed
    1. Pütz J, et al. FEBS Lett. 2010;584:350. - PubMed
    1. Shawan MMAK, et al. Data in Brief. 2016;9:602. - PubMed

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