Bioinformatics Database Resources

Khandelwal, Icxa; Sharma, Aditi; Agrawal, P. K.; Shrivastava, Rahul

doi:10.4018/978-1-5225-1871-6.ch004

Cited by 4 publications

(4 citation statements)

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“…Bioinformatics analysis of the obtained nucleotide sequence using BLASTn did not show significant homology with other mycobacteria, hence, BLASTx was used to analyze the sequence. As protein sequence is more conserved in comparison to nucleotide sequence on the basis of evolutionary relationship, BLASTx translates nucleotide sequence into protein to identify homologous proteins (Khandelwal et al 2017). Homology study carried out with the translated protein sequence led to identification of putative ribosomal maturation factor 'RimP' of M. fortuitum (MfRimP) as the mutated gene, on the basis of closest homology to the RimP protein of M. abscessus subspecies abscessus.…”

Section: Discussionmentioning

confidence: 99%

Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions

et al. 2019

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Mycobacterium fortuitum is an important human pathogenic NTM, which resists stress conditions inside macrophages by exploitation of specific genes. TnphoA-based transposon mutagenesis was employed to identify membrane genes responsible for survival of M. fortuitum under such stress conditions. A library of about 450 mutants was constructed after electroporation of vector pRT291 into wild-type M. fortuitum. On the basis of blue color development and alkaline phosphatase assay, 20 mutants were shortlisted to screen for growth and survival under acidic stress at pH 6.5, 5.5, 4.5, and 3.5. Mutant MT727 showed reduced growth and survival under acidic stress. The acid susceptible mutant MT727 was subjected to other in vitro stress conditions prevalent inside macrophages including oxidative, nutrient starvation and nitrosative stress. However, the mutant showed no appreciable difference in growth behavior under oxidative, nutrient starvation and nitrosative stress conditions in comparison to the wild type. Genomic and bioinformatics analysis of MT727 led to identification of putative ribosomal maturation factor RimP of M. fortuitum to be affected by mutagenesis, showing closest homology to M. abscessus RimP. In silico functional interaction of RimP protein using STRING database showed its interaction with proteins of ribosomal assembly and maturation. Results indicate role of rimP gene in survival of M. fortuitum under acidic stress conditions which may be further explored for use as a potential drug target against M. fortuitum and other mycobacterial infections.

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Section: Discussionmentioning

confidence: 99%

Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions

et al. 2019

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“…Some popular biological data set are GenBank, Protein Data bank etc. (Herbert et al, 2007;Khandelwal et al, 2017), Data miningtechniquesarereadytoacceptthestatedchallengesinthefieldofbioinformatics.Withthe significantprogressinbiologicaldata,dataminingorKDDwillplayasubstantialroleinevaluating thedataandinsolvingevolvingproblemsandchallengesinbioinformatics (Wangetal.,2005).…”

Section: Challenges In Bioinformaticsmentioning

confidence: 99%

Role of Data Mining Techniques in Bioinformatics

Singh¹,

Singh²

2021

International Journal of Applied Research in Bioinformatics

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Data mining offers a highly effective technique that is useful in research and development of bioinformatics. Bioinformatics consists biological information such as DNA, RNA, and protein. Data mining tasks/techniques are classification, prediction, clustering, association, outlier detection, regression, and pattern tracking. Data mining provides important correlation, hidden patterns, and knowledge from the bioinformatics data set. This paper presents the role of data mining techniques in bioinformatics application. Classification of gene and protein structure, analyzing the gene expression, association of co-disease, outlier detection and gene selection, protein structure prediction, and drug discovery are some typical biological example that has proven data mining as a suitable technique for bioinformatics.

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“…BLAST is a tool used to compare sequences of various types of organisms. The score of each alignment is given an expectation value (E value), which is a measure of statistical significance [54].…”

Section: Binningmentioning

confidence: 99%

“…Pfam's analysis refers to the double alignment produced using the hidden Markov model. The purpose of Pfam's analysis is to look at the relationship between protein sequences at the family level [54].…”

Section: Pfam Analysismentioning

confidence: 99%

Metagenomic applications in exploration and development of novel enzymes from nature: a review

Prayogo

Budiharjo

Kusumaningrum

et al. 2020

Journal of Genetic Engineering and Biotechnology

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Background: Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. The main body of the abstract: Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research. Short conclusion: Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.

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Bioinformatics Database Resources

Cited by 4 publications

References 58 publications

Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions

Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions

Role of Data Mining Techniques in Bioinformatics

Metagenomic applications in exploration and development of novel enzymes from nature: a review

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