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AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals

The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a...

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Detalles Bibliográficos
Autores principales: Kosiński, Jan G., Żywicki, Marek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621952/
https://www.ncbi.nlm.nih.gov/pubmed/37851672
http://dx.doi.org/10.1371/journal.pcbi.1011527
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author Kosiński, Jan G.
Żywicki, Marek
author_facet Kosiński, Jan G.
Żywicki, Marek
author_sort Kosiński, Jan G.
collection PubMed
description The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows.
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spelling pubmed-106219522023-11-03 AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals Kosiński, Jan G. Żywicki, Marek PLoS Comput Biol Software The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation of such results is essential for researchers to draw conclusions from obtained results. Although some tools are available, their functionality is limited. Here, we present AGouTI–a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals and can be used on custom column-based text files obtained from different data analysis pipelines. Although providing many unique options, AGouTI is straightforward in installation and usage, enabling effortless integration into existing data analysis workflows. Public Library of Science 2023-10-18 /pmc/articles/PMC10621952/ /pubmed/37851672 http://dx.doi.org/10.1371/journal.pcbi.1011527 Text en © 2023 Kosiński, Żywicki https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Software
Kosiński, Jan G.
Żywicki, Marek
AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title_full AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title_fullStr AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title_full_unstemmed AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title_short AGouTI–Flexible Annotation of Genomic and Transcriptomic Intervals
title_sort agouti–flexible annotation of genomic and transcriptomic intervals
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10621952/
https://www.ncbi.nlm.nih.gov/pubmed/37851672
http://dx.doi.org/10.1371/journal.pcbi.1011527
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