Abstract
In this paper, we presented the datasets generated using Chose Game representation (CGR) and Choase Game Representation of Frequencies (FCGR) of bacterial and archaeal 16S rRNA sequences. The data in the form of graphical representations was yielded with the help of ENDMEMO tool. The computational representation of these data datasets is useful for studies and interpretation of microbial sequences. Based on a technique from chaotic dynamics, the method produces a picture of any gene (DNA and RNA) sequence which displays both local and global patterns. Eukaryotes and prokaryotes can be identified merely based on their generated visual representation/DNA structures.
Keywords: Chilka Lake, ENDMEMO, Halophiles, Sambhar Lake, 16S rRNA
Specifications Table
| Subject area | Biology |
| More specific subject area | Microbiology; Bioinformatics |
| Type of data | Table, figure |
| How data was acquired | Bioinformatics tools |
| Data format | Raw, analyzed |
| Experimental factors | Standard and default |
| Experimental features | Graphical representations |
| Data source location | School of Life Sciences, SRTM University, Nanded |
| Data accessibility | Data is available with this article |
Value of the data
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Data generated in this study permits the representation and investigation of patterns in any type of sequences which visually revealed previously unknown pattern.
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The generated graphical data by means of sequences using a new tool derived from the "chaotic dynamical systems" which allowed the depiction of frequencies of oligonucleotides in the form of images.
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Data on CGR and FCGR are the main factors explaining the variability observed among sequences. The distance between images helpful for measurement of phylogenetic proximity.
1. Data
This paper describes data on 16S rRNA sequence of bacterial and archaeal species isolated from Soda Lakes such as Sambhar Lake and Chilka Lake (India). The data generated in the form of graphical representations contains information on their oligonucleotides distribution and numbers.
2. Experimental design, materials and methods
115 bacterial and archaeal 16S rRNA sequences (both short and long) were obtained in FASTA format from NCBI repository (Table 1). These sequences of bacteria and archaea were used for graphical representations. The generated graphical representations in the form of Chaose Game Representations (Fig. 1) and Chose Game Representations of Frequencies (Fig. 2) obtained in the form of visual images [1], [2]. Graphical representations of oligonucleotides in the form of CGR and FCGR pictorial representations were created using ENDMEMO tool [3], [4] for studies on primary sequence organization and representation of oligonucleotides frequency in the given sequence.
Table 1.
Bacterial and archaeal species isolated from Soda Lakes.
| Accession number | Species/Strain |
|---|---|
| AF472595 | Sambhar Salt Lake archaeon HA1 |
| AF472596 | Sambhar Salt Lake archaeon HA6 |
| AJ889020 | Marichromatium chilcum |
| EU669822 | Haloalkaliphilic bacterium EMB4 |
| FJ984520 | Marinobacter alkaliphilus strain NBSL05 |
| FJ984521 | Marinobacter alkaliphilus strain NBSL06 |
| FJ984522 | Marinobacter hydrocarbonoclasticus strain NBSL04 |
| FJ984523 | Halomonas sp. NBSL08 |
| FJ984524 | Marinobacter alkaliphilus strain NBSL03 |
| FJ984525 | Halomonas sp. NBSL10 |
| FJ984526 | Halomonas sp. NBSL14 |
| FJ984527 | Tsukamurella sp. NBSL21 |
| FJ984528 | Ochrobactrum haemophilum strain NBSL23 |
| FJ984529 | Bacillus horikoshii strain NBSL26 |
| FJ984530 | Bacillus horikoshii strain NBSL27 |
| FJ984531 | Micrococcus luteus strain NBSL29 |
| FJ984532 | Halomonas sp. NBSL09 |
| FJ984533 | Micrococcus luteus strain NBSL28 |
| GQ227415 | Methylobacterium radiotolerans strain NBCS1 |
| GQ281064 | Hyphomicrobium facile strain NBCS26 |
| GQ281065 | Methylobacterium zatmanii strain NBCS25 |
| GQ281066 | Hyphomicrobium facile strain NBCS23 |
| GQ281070 | Mycobacterium brisbanense strain NBCS10 |
| GQ281073 | Pseudomonas sp. NBCS06 |
| GQ281075 | Hyphomicrobium facile strain NBCS7 |
| GQ354269 | Methylobacterium radiotolerans strain NBCS3 |
| GQ411500 | Methylobacterium extorquens strain NBCS16 |
| GQ411502 | Methylobacterium sp. NBCS19 |
| GQ411503 | Methylobacterium radiotolerans strain NBCS21 |
| GQ411505 | Methylobacterium sp. NBCS20 |
| GQ411539 | Uncultured Streptosporangium sp. clone 62 |
| GQ411540 | Uncultured Streptosporangium sp. clone 61 |
| GQ411541 | Uncultured Streptosporangium sp. clone 64 |
| GQ411542 | Uncultured Streptosporangium sp. clone 63 |
| JF343124 | Staphylococcus sp. IARI-CS-2 |
| JF343125 | Acinetobacter johnsonii strain IARI-CS-7 |
| JF343126 | Acinetobacter venetianus strain IARI-CS-13 |
| JF343127 | Acinetobacter sp. IARI-CS-15 |
| JF343128 | Acinetobacter sp. IARI-CS-17 |
| JF343129 | Micrococcus luteus strain IARI-CS-18 |
| JF343130 | Agromyces sp. IARI-CS-28 |
| JF343132 | Micrococcus indicus strain IARI-CS-31 |
| JF343133 | Staphylococcus haemolyticus strain IARI-CS-32 |
| JF343139 | Bacillus mycoides strain IARI-CS-41 |
| JF343140 | Bacillus altitudinis strain IARI-CS-43 |
| JF343144 | Acinetobacter venetianus strain IARI-CS-50 |
| JF343145 | Acinetobacter venetianus strain IARI-CS-51 |
| JF343152 | Staphylococcus arlettae strain IARI-CS-60 |
| JF343153 | Pseudomonas stutzeri strain IARI-CS-62 |
| JF343157 | Exiguobacterium sp. IARI-CS-68 |
| JF343158 | Exiguobacterium indicum strain IARI-CS-69 |
| JF343162 | Micrococcus yunnanensis strain IARI-CS-16 |
| JF343163 | Sphingomonas melonis strain IARI-CW-25 |
| JF343165 | Stenotrophomonas sp. IARI-CW-51 |
| JF343167 | Staphylococcus equorum strain IARI-CW-11 |
| JF343170 | Pseudomonas aeruginosa strain IARI-CW-30 |
| JN411473 | Stenotrophomonas sp. IARI-CW-52 |
| JN411475 | Stenotrophomonas sp. IARI-CW-55 |
| JQ328187 | Natronococcus sp. SLA-60 |
| JQ328188 | Natronococcus occultus strain SLA-2 |
| JQ328189 | Natronococcus sp. SLA-3 |
| JX428952 | Halobacillus sp. IARI-ABCL-1 |
| JX428953 | Nesterenkonia halophila strain IARI-ABCL-4 |
| JX428954 | Halococcus sp. IARI-ABCL-7 |
| JX428955 | Brachybacterium sp. IARI-ABCL-8 |
| JX428956 | Pontibacillus sp. IARI-ABCL-9 |
| JX428957 | Virgibacillus halodenitrificans strain IARI-ABK-2 |
| JX428958 | Marinococcus halophilus strain IARI-ABK-3 |
| JX428959 | Haladaptatus paucihalophilus strain IARI-ABK-4 |
| KC434452 | Halomonas sp. SSL5 |
| KC434453 | Halomonas venusta strain SSL6 |
| KC434454 | Oceanobacillus sp. SSL7 |
| KC434455 | Natronococcus xinjiangense strain SLA61 |
| KC434456 | Halomonas pantelleriensis strain SSL8 |
| KC434457 | Natronorubrum thiooxidans strain SLA62 |
| KC440854 | Bacillus sp. SSL1 |
| KC440855 | Bacillus cereus strain SSL2 |
| KC696560 | Natronococcus occultus strain SLA64 |
| KC696561 | Natronococcus sp. SSL9 |
| KC820814 | Natronococcus jeotgali strain SLA63 |
| KC924847 | Euhalothece sp. SLVH01 |
| KC934935 | Nesterenkonia sp. SSL10 |
| KC934936 | Halomonas sp. SSL11 |
| KC934937 | Oceanobacillus iheyensis strain SSL12 |
| KC934938 | Halomonas alkaliphila strain SSL13 |
| KC934939 | Halomonas sp. SSL14 |
| KC934940 | Halomonas pantelleriensis strain SSL15 |
| KC934941 | Staphylococcus sp. SSL16 |
| KF288960 | Halomonas sp. SSL3 |
| KF288961 | Halomonas pantelleriensis strain SSL4 |
| KU179507 | Microbacterium sp. ANSKSlab01 |
| KU518891 | Paenibacillus dendritiformis strain ANSKLAB02 |
| KU529483 | Bacillus tequilensis strain ANSKLAB04 |
| LT161878 | Paenibacillus sp. SMB1 |
| LT161879 | Halomonas sp. SMB2 |
| LT161880 | Halomonas sp. SMB3 |
| LT161881 | Bacillus sp. SMB4 |
| LT161882 | Bacillus sp. SMB5 |
| LT161883 | Bacillus sp. SMB6 |
| LT161884 | Halomonas sp. SMB7 |
| LT222351 | Halomonas sp. SMB8 |
| LT599833 | Exiguobacterium sp. SMB10 |
| NZ_MASN01000022 | Natrialba sp. SSL1 ctg29 |
| NZ_MASN01000031 | Natrialba sp. SSL1 ctg37 |
| NZ_MASN01000032 | Natrialba sp. SSL1 ctg38 |
| NZ_MASN01000033 | Natrialba sp. SSL1 ctg39 |
| NZ_MASN01000042 | Natrialba sp. SSL1 ctg47 |
| NZ_MASN01000044 | Natrialba sp. SSL1 ctg49 |
| NZ_MASN01000045 | Natrialba sp. SSL1 ctg5 |
| NZ_MASN01000046 | Natrialba sp. SSL1 ctg50 |
| NZ_MASN01000047 | Natrialba sp. SSL1 ctg51 |
| NZ_MASN01000049 | Natrialba sp. SSL1 ctg53 |
| NZ_MASN01000053 | Natrialba sp. SSL1 ctg57 |
| NZ_MASN01000054 | Natrialba sp. SSL1 ctg58 |
| NZ_MASN01000055 | Natrialba sp. SSL1 ctg59 |
| NZ_MASN01000057 | Natrialba sp. SSL1 ctg60 |
| NZ_MASN01000058 | Natrialba sp. SSL1 ctg61 |
Acknowledgments
BNR is thankful to University Grants Commission, New Delhi (India) for the financial support in the form postdoctoral fellowship for this research (Grant no. PDFSS-2013-14-ST-MAH-4350).
Footnotes
Transparency data associated with this article can be found in the online version at doi:10.1016/j.dib.2017.03.017.
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2017.03.017.
Transparency document. Supplementary material
Supplementary material
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Appendix A. Supplementary material
Supplementary material.
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