Literature DB >> 28393088

Data on graphical representation (CGR and FCGR) of bacterial and archaeal species from two Soda Lakes.

Bhagwan N Rekadwad1, Chandrahasya N Khobragade1.   

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.

Entities:  

Keywords:  16S rRNA; Chilka Lake; ENDMEMO; Halophiles; Sambhar Lake

Year:  2017        PMID： 28393088      PMCID： PMC5376247          DOI： 10.1016/j.dib.2017.03.017

Source DB:  PubMed          Journal:  Data Brief        ISSN： 2352-3409


Specifications Table Value of the data Data generated in this study permits the representation and investigation of patterns in any type of sequences which visually revealed previously unknown pattern. 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. 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.

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.

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 numberSpecies/Strain
AF472595Sambhar Salt Lake archaeon HA1
AF472596Sambhar Salt Lake archaeon HA6
AJ889020Marichromatium chilcum
EU669822Haloalkaliphilic bacterium EMB4
FJ984520Marinobacter alkaliphilus strain NBSL05
FJ984521Marinobacter alkaliphilus strain NBSL06
FJ984522Marinobacter hydrocarbonoclasticus strain NBSL04
FJ984523Halomonas sp. NBSL08
FJ984524Marinobacter alkaliphilus strain NBSL03
FJ984525Halomonas sp. NBSL10
FJ984526Halomonas sp. NBSL14
FJ984527Tsukamurella sp. NBSL21
FJ984528Ochrobactrum haemophilum strain NBSL23
FJ984529Bacillus horikoshii strain NBSL26
FJ984530Bacillus horikoshii strain NBSL27
FJ984531Micrococcus luteus strain NBSL29
FJ984532Halomonas sp. NBSL09
FJ984533Micrococcus luteus strain NBSL28
GQ227415Methylobacterium radiotolerans strain NBCS1
GQ281064Hyphomicrobium facile strain NBCS26
GQ281065Methylobacterium zatmanii strain NBCS25
GQ281066Hyphomicrobium facile strain NBCS23
GQ281070Mycobacterium brisbanense strain NBCS10
GQ281073Pseudomonas sp. NBCS06
GQ281075Hyphomicrobium facile strain NBCS7
GQ354269Methylobacterium radiotolerans strain NBCS3
GQ411500Methylobacterium extorquens strain NBCS16
GQ411502Methylobacterium sp. NBCS19
GQ411503Methylobacterium radiotolerans strain NBCS21
GQ411505Methylobacterium sp. NBCS20
GQ411539Uncultured Streptosporangium sp. clone 62
GQ411540Uncultured Streptosporangium sp. clone 61
GQ411541Uncultured Streptosporangium sp. clone 64
GQ411542Uncultured Streptosporangium sp. clone 63
JF343124Staphylococcus sp. IARI-CS-2
JF343125Acinetobacter johnsonii strain IARI-CS-7
JF343126Acinetobacter venetianus strain IARI-CS-13
JF343127Acinetobacter sp. IARI-CS-15
JF343128Acinetobacter sp. IARI-CS-17
JF343129Micrococcus luteus strain IARI-CS-18
JF343130Agromyces sp. IARI-CS-28
JF343132Micrococcus indicus strain IARI-CS-31
JF343133Staphylococcus haemolyticus strain IARI-CS-32
JF343139Bacillus mycoides strain IARI-CS-41
JF343140Bacillus altitudinis strain IARI-CS-43
JF343144Acinetobacter venetianus strain IARI-CS-50
JF343145Acinetobacter venetianus strain IARI-CS-51
JF343152Staphylococcus arlettae strain IARI-CS-60
JF343153Pseudomonas stutzeri strain IARI-CS-62
JF343157Exiguobacterium sp. IARI-CS-68
JF343158Exiguobacterium indicum strain IARI-CS-69
JF343162Micrococcus yunnanensis strain IARI-CS-16
JF343163Sphingomonas melonis strain IARI-CW-25
JF343165Stenotrophomonas sp. IARI-CW-51
JF343167Staphylococcus equorum strain IARI-CW-11
JF343170Pseudomonas aeruginosa strain IARI-CW-30
JN411473Stenotrophomonas sp. IARI-CW-52
JN411475Stenotrophomonas sp. IARI-CW-55
JQ328187Natronococcus sp. SLA-60
JQ328188Natronococcus occultus strain SLA-2
JQ328189Natronococcus sp. SLA-3
JX428952Halobacillus sp. IARI-ABCL-1
JX428953Nesterenkonia halophila strain IARI-ABCL-4
JX428954Halococcus sp. IARI-ABCL-7
JX428955Brachybacterium sp. IARI-ABCL-8
JX428956Pontibacillus sp. IARI-ABCL-9
JX428957Virgibacillus halodenitrificans strain IARI-ABK-2
JX428958Marinococcus halophilus strain IARI-ABK-3
JX428959Haladaptatus paucihalophilus strain IARI-ABK-4
KC434452Halomonas sp. SSL5
KC434453Halomonas venusta strain SSL6
KC434454Oceanobacillus sp. SSL7
KC434455Natronococcus xinjiangense strain SLA61
KC434456Halomonas pantelleriensis strain SSL8
KC434457Natronorubrum thiooxidans strain SLA62
KC440854Bacillus sp. SSL1
KC440855Bacillus cereus strain SSL2
KC696560Natronococcus occultus strain SLA64
KC696561Natronococcus sp. SSL9
KC820814Natronococcus jeotgali strain SLA63
KC924847Euhalothece sp. SLVH01
KC934935Nesterenkonia sp. SSL10
KC934936Halomonas sp. SSL11
KC934937Oceanobacillus iheyensis strain SSL12
KC934938Halomonas alkaliphila strain SSL13
KC934939Halomonas sp. SSL14
KC934940Halomonas pantelleriensis strain SSL15
KC934941Staphylococcus sp. SSL16
KF288960Halomonas sp. SSL3
KF288961Halomonas pantelleriensis strain SSL4
KU179507Microbacterium sp. ANSKSlab01
KU518891Paenibacillus dendritiformis strain ANSKLAB02
KU529483Bacillus tequilensis strain ANSKLAB04
LT161878Paenibacillus sp. SMB1
LT161879Halomonas sp. SMB2
LT161880Halomonas sp. SMB3
LT161881Bacillus sp. SMB4
LT161882Bacillus sp. SMB5
LT161883Bacillus sp. SMB6
LT161884Halomonas sp. SMB7
LT222351Halomonas sp. SMB8
LT599833Exiguobacterium sp. SMB10
NZ_MASN01000022Natrialba sp. SSL1 ctg29
NZ_MASN01000031Natrialba sp. SSL1 ctg37
NZ_MASN01000032Natrialba sp. SSL1 ctg38
NZ_MASN01000033Natrialba sp. SSL1 ctg39
NZ_MASN01000042Natrialba sp. SSL1 ctg47
NZ_MASN01000044Natrialba sp. SSL1 ctg49
NZ_MASN01000045Natrialba sp. SSL1 ctg5
NZ_MASN01000046Natrialba sp. SSL1 ctg50
NZ_MASN01000047Natrialba sp. SSL1 ctg51
NZ_MASN01000049Natrialba sp. SSL1 ctg53
NZ_MASN01000053Natrialba sp. SSL1 ctg57
NZ_MASN01000054Natrialba sp. SSL1 ctg58
NZ_MASN01000055Natrialba sp. SSL1 ctg59
NZ_MASN01000057Natrialba sp. SSL1 ctg60
NZ_MASN01000058Natrialba sp. SSL1 ctg61
Subject areaBiology
More specific subject areaMicrobiology; Bioinformatics
Type of dataTable, figure
How data was acquiredBioinformatics tools
Data formatRaw, analyzed
Experimental factorsStandard and default
Experimental featuresGraphical representations
Data source locationSchool of Life Sciences, SRTM University, Nanded
Data accessibilityData is available with this article
  4 in total

1.  Genomic signature: characterization and classification of species assessed by chaos game representation of sequences.

Authors:  P J Deschavanne; A Giron; J Vilain; G Fagot; B Fertil
Journal:  Mol Biol Evol       Date:  1999-10       Impact factor: 16.240

2.  Chaos game representation of gene structure.

Authors:  H J Jeffrey
Journal:  Nucleic Acids Res       Date:  1990-04-25       Impact factor: 16.971

3.  Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.

Authors:  Bhagwan N Rekadwad; Juan M Gonzalez; Chandrahasya N Khobragade
Journal:  Biomed Res Int       Date:  2016-11-01       Impact factor: 3.411

4.  Digital data for Quick Response (QR) codes of thermophiles to identify and compare the bacterial species isolated from Unkeshwar hot springs (India).

Authors:  Bhagwan N Rekadwad; Chandrahasya N Khobragade
Journal:  Data Brief       Date:  2015-11-24
  4 in total
  1 in total

1.  Bioinformatics delimitation of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Southern Ocean.

Authors:  Palaniappan Sivasankar; Bhagwan Rekadwad; Subramaniam Poongodi; Kannan Sivakumar; Bhaskar Venkateswaran Parli; N Anil Kumar
Journal:  Data Brief       Date:  2018-03-08
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.