peaks2utr: a robust Python tool for the annotation of 3′ UTRs

SUMMARY: Annotation of nonmodel organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present...

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Detalles Bibliográficos
Autores principales: Haese-Hill, William, Crouch, Kathryn, Otto, Thomas D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008064/
https://www.ncbi.nlm.nih.gov/pubmed/36864613
http://dx.doi.org/10.1093/bioinformatics/btad112
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author Haese-Hill, William
Crouch, Kathryn
Otto, Thomas D
author_facet Haese-Hill, William
Crouch, Kathryn
Otto, Thomas D
author_sort Haese-Hill, William
collection PubMed
description SUMMARY: Annotation of nonmodel organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single-cell technologies, such as 10× Chromium, to accurately annotate 3′ UTRs for a given canonical annotation. AVAILABILITY AND IMPLEMENTATION: peaks2utr is implemented in Python 3 (≥3.8). It is available via PyPI at https://pypi.org/project/peaks2utr and GitHub at https://github.com/haessar/peaks2utr. It is licensed under GNU GPLv3.
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spelling pubmed-100080642023-03-12 peaks2utr: a robust Python tool for the annotation of 3′ UTRs Haese-Hill, William Crouch, Kathryn Otto, Thomas D Bioinformatics Applications Note SUMMARY: Annotation of nonmodel organisms is an open problem, especially the detection of untranslated regions (UTRs). Correct annotation of UTRs is crucial in transcriptomic analysis to accurately capture the expression of each gene yet is mostly overlooked in annotation pipelines. Here we present peaks2utr, an easy-to-use Python command line tool that uses the UTR enrichment of single-cell technologies, such as 10× Chromium, to accurately annotate 3′ UTRs for a given canonical annotation. AVAILABILITY AND IMPLEMENTATION: peaks2utr is implemented in Python 3 (≥3.8). It is available via PyPI at https://pypi.org/project/peaks2utr and GitHub at https://github.com/haessar/peaks2utr. It is licensed under GNU GPLv3. Oxford University Press 2023-03-02 /pmc/articles/PMC10008064/ /pubmed/36864613 http://dx.doi.org/10.1093/bioinformatics/btad112 Text en © The Author(s) 2023. Published by Oxford University Press. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Haese-Hill, William
Crouch, Kathryn
Otto, Thomas D
peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title_full peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title_fullStr peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title_full_unstemmed peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title_short peaks2utr: a robust Python tool for the annotation of 3′ UTRs
title_sort peaks2utr: a robust python tool for the annotation of 3′ utrs
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008064/
https://www.ncbi.nlm.nih.gov/pubmed/36864613
http://dx.doi.org/10.1093/bioinformatics/btad112
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