Journal of Pulmonology and Clinical Research

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Perspective - Journal of Pulmonology and Clinical Research (2023) Volume 6, Issue 2

Performances of bioinformatics tools for the Mycobacterium tuberculosis complex strains

Robert Brown*

Department of Bioinformatics, University of Maryland, United states

*Corresponding Author:
Robert Brown
Department of Bioinformatics
University of Maryland
United states
E-mail:sophie@kates.au.in

Received: 26-Feb-2023, Manuscript No. AAJPCR-23-94581; Editor assigned: 28-Feb-2023, PreQC No. AAJPCR-23-94581(PQ); Reviewed: 14-Mar-2023, QC No. AAJPCR-23-94573Revised: 19-Mar-2023, Manuscript No. AAJPCR-23-94581(R); Published: 26-Mar-2023, DOI:10.35841/aajpcr-6.2.140

Citation: Brown R. Performances of bioinformatics tools for the Mycobacterium tuberculosis complex strains. J Pulmonol Clin Res. 2023;6(2):140

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Abstract

  

Introduction

Mycobacterium Tuberculosis Complex (MTBC) strains are a group of closely related bacteria that cause Tuberculosis (TB) in humans and other animals. There are several different strains of MTBC, each with slightly different genetic characteristics. Which is responsible for the vast majority of TB cases in humans? Other strains of MTBC include M. bovis, which can infect both humans and animals, and M. africanum, which is found primarily in West Africa. In addition to these three primary strains, there are also several other MTBC strains that have been identified, including M. canettii, M. microti, and M. caprae, among others. Each of these strains has slightly different genetic characteristics and can cause slightly different symptoms in infected individuals. It's worth noting that MTBC strains can also develop drug resistance, which can make treating TB more difficult.[1].

Multi-Drug-Resistant (MDR) and extensively drug-resistant strains of MTBC are becoming increasingly common, particularly in areas where TB is endemic and treatment options are limited. Mycobacterium tuberculosis complex strains are a group of bacteria that cause tuberculosis, a serious infectious disease that mainly affects the lungs but can also affect other parts of the body. The Mycobacterium tuberculosis complex includes several species of mycobacteria, including Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium africanum. These bacteria are highly contagious and can be transmitted through the air when an infected person coughs or sneezes. Mycobacterium tuberculosis is the most common species of the complex and is responsible for the majority of TB cases worldwide. Mycobacterium bovis is also a significant cause of TB in some countries, particularly those with a high prevalence of bovine TB. Mycobacterium africanum is primarily found in West Africa, where it is responsible for a significant proportion of TB cases.[2].

Mycobacterium tuberculosis complex strains are known for their ability to survive for long periods in the environment and to evade the human immune system, which makes TB a challenging disease to treat and control.There are many bioinformatics tools available for analyzing the genome of Mycobacterium tuberculosis complex strains. The performance of these tools can vary depending on the specific analysis being performed, the quality and completeness of the genome assembly, and the specific strains being analyzed. Here are some commonly used bioinformatics tools for analyzing Mycobacterium tuberculosis complex strains and their performance characteristics: Genome assemblers: Assembling the genome is the first step in analyzing the genomic data. Some commonly used genome assemblers for Mycobacterium tuberculosis complex strains are SPAdes, Canu, and Flye. These assemblers are known to produce high-quality assemblies for complex genomes. Annotation tools: After the genome is assembled, it needs to be annotated to identify the genes and other functional elements. Tools such as Prokka and RAST are commonly used for genome annotation of Mycobacterium tuberculosis complex strains.[3].

Variant callers are used to identify Single Nucleotide Polymorphisms (SNPs) and other genetic variations. Some commonly used variant callers for Mycobacterium tuberculosis complex strains are GATK, FreeBayes, and VarScan. Phylogenetic analysis tools Phylogenetic analysis is used to study the evolutionary relationships between different strains of Mycobacterium tuberculosis complex. Tools such as RAxML and IQ-TREE are commonly used for this analysis. Drug resistance prediction tools: Mycobacterium tuberculosis complex strains can develop resistance to multiple drugs, which can complicate treatment. Tools such as TBProfiler and Mykrobe Predictor are commonly used for predicting drug resistance based on the genome sequence. Overall, the performance of these tools depends on many factors, such as the quality of the input data, the specific analysis being performed, and the specific strains being analyzed. It is important to carefully select and validate the bioinformatics tools for the specific analysis being performed to ensure the accuracy and reliability of the results.[4].

Variant callers are used to identify Single Nucleotide Polymorphisms (SNPs) and other genetic variations. Some commonly used variant callers for Mycobacterium tuberculosis complex strains are GATK, FreeBayes, and VarScan. Phylogenetic analysis tools Phylogenetic analysis is used to study the evolutionary relationships between different strains of Mycobacterium tuberculosis complex. Tools such as RAxML and IQ-TREE are commonly used for this analysis. Drug resistance prediction tools: Mycobacterium tuberculosis complex strains can develop resistance to multiple drugs, which can complicate treatment. Tools such as TBProfiler and Mykrobe Predictor are commonly used for predicting drug resistance based on the genome sequence. Overall, the performance of these tools depends on many factors, such as the quality of the input data, the specific analysis being performed, and the specific strains being analyzed. It is important to carefully select and validate the bioinformatics tools for the specific analysis being performed to ensure the accuracy and reliability of the results.[5].

References

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