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TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation...

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Detalles Bibliográficos
Autores principales: Sohrab, Vista, López-Díaz, Cristina, Di Pietro, Antonio, Ma, Li-Jun, Ayhan, Dilay Hazal
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7914406/
https://www.ncbi.nlm.nih.gov/pubmed/33557410
http://dx.doi.org/10.3390/genes12020224
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author Sohrab, Vista
López-Díaz, Cristina
Di Pietro, Antonio
Ma, Li-Jun
Ayhan, Dilay Hazal
author_facet Sohrab, Vista
López-Díaz, Cristina
Di Pietro, Antonio
Ma, Li-Jun
Ayhan, Dilay Hazal
author_sort Sohrab, Vista
collection PubMed
description Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis.
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spelling pubmed-79144062021-03-01 TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data Sohrab, Vista López-Díaz, Cristina Di Pietro, Antonio Ma, Li-Jun Ayhan, Dilay Hazal Genes (Basel) Article Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinformatics software to identify insertion events. However, the application of existing tools is limited by either narrow-focused design of the package, too many dependencies on other tools, or prior knowledge required as input files that may not be readily available to all users. Here, we reported a simple pipeline, TEfinder, developed for the detection of new TE insertions with minimal software and input file dependencies. The external software requirements are BEDTools, SAMtools, and Picard. Necessary input files include the reference genome sequence in FASTA format, an alignment file from paired-end reads, existing TEs in GTF format, and a text file of TE names. We tested TEfinder among several evolving populations of Fusarium oxysporum generated through a short-term adaptation study. Our results demonstrate that this easy-to-use tool can effectively detect new TE insertion events, making it accessible and practical for TE analysis. MDPI 2021-02-04 /pmc/articles/PMC7914406/ /pubmed/33557410 http://dx.doi.org/10.3390/genes12020224 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sohrab, Vista
López-Díaz, Cristina
Di Pietro, Antonio
Ma, Li-Jun
Ayhan, Dilay Hazal
TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title_full TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title_fullStr TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title_full_unstemmed TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title_short TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data
title_sort tefinder: a bioinformatics pipeline for detecting new transposable element insertion events in next-generation sequencing data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7914406/
https://www.ncbi.nlm.nih.gov/pubmed/33557410
http://dx.doi.org/10.3390/genes12020224
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