Genomics dataset on unclassified published organism (patent US 7547531)

Abstract

Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR) code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5%) which was followed by GP445198 (61.8%) and GP445189 (59.44%), while lowest was in GP445178 (24.39%). In addition, New England BioLabs (NEB) database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms’ hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

Genomics dataset of unidentified disclosed isolates

“…It gives exact information about cleavage affected CpG methylation and other types of methylation possible caused by biomolcules. Additionally, BioLabs database determined the AT and GC percentage in the genome [7] , [8] ( Fig. 3 ; Table 1 ).…”

Characteristics and Lytic Activity of Phage-Derived Peptidoglycan Hydrolase, LysSAP8, as a Potent Alternative Biocontrol Agent for Staphylococcus aureus

“…The predicted ORFs were annotated using Blastp based on the e-value < 1E-05, and classified into six groups based on their functions: packaging, structure, host lysis, DNA manipulation, DNA regulation, and additional function. The G+C content was predicted using the DNA/RNA GC content calculator from ENDMEMO (http://www.endme mo.com/bio/gc.php), and the tRNAscan-SE 1.21 (The Lowe Lab, University of California Santa Cruz, USA) was used to search for the tRNA [27,28].…”

tRNA diversification among uncultured archeon clones

“…Complete DNA sequences of four uncultured archeon clones were retrieved from NCBI (National Center for Biotechnology Information) BioSample database via Nucleotide DNA database and stored in FASTA format [ 5 ]. Detected tRNAs were classified into different classes based on amino acid code and cove score [ 6 , 7 , 8 , 9 ].…”