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Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Applications of Molecular Taxonomy01:20

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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

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Published on: June 28, 2018

MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms.

Nicolás Tomasini1, Juan J Lauthier, Martin S Llewellyn

  • 1Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
|September 13, 2013
PubMed
Summary
This summary is machine-generated.

A new software, MLSTest, is introduced for analyzing multi-locus sequence typing (MLST) data, especially for diploid eukaryotes. It offers novel methods for genetic exchange analysis, tree construction, and optimizing typing schemes, improving microorganism genotyping.

Keywords:
ConcatenationIncongruenceMLSTMLSTestMulti-locus sequence typingSoftware

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Novel Sequence Discovery by Subtractive Genomics
09:40

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Published on: January 25, 2019

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genetics

Background:

  • Multi-locus sequence typing (MLST) is a standard for bacterial pathogen genotyping.
  • Existing MLST tools are limited for analyzing diploid eukaryotic sequence data.
  • There is a need for advanced software to handle complex eukaryotic MLST data.

Purpose of the Study:

  • To introduce MLSTest, a novel software for MLST data analysis, specifically designed for diploid eukaryotes.
  • To provide enhanced functionalities for evaluating MLST datasets, including genetic exchange and tree construction.
  • To offer tools for developing and optimizing MLST schemes for improved discriminatory power.

Main Methods:

  • Development of MLSTest software incorporating standard and novel MLST analysis methods.
  • Implementation of algorithms for allelic profile construction, clustering, and BURST graph analysis.
  • Inclusion of tree construction methods for heterozygous/three-state sites and incongruence analysis.

Main Results:

  • MLSTest successfully analyzes diploid eukaryotic MLST data, addressing limitations of existing tools.
  • The software provides robust methods for evaluating genetic exchange and constructing phylogenetic trees.
  • Tests for locus combination suitability and optimization of typing schemes were evaluated on simulated and real datasets.

Conclusions:

  • MLSTest is a valuable tool for eukaryotic MLST data analysis and the development of novel typing schemes.
  • The software enhances the ability to study genetic diversity and population structures in microorganisms.
  • MLSTest offers a comprehensive solution for complex MLST data challenges in both bacterial and eukaryotic pathogens.