CONCUR: quick and robust calculation of codon usage from ribosome profiling data

SUMMARY: CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. AVAILABILITY AND IMPLEMENTATION: CONCUR is written in Perl and is freely...

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Detalles Bibliográficos
Autores principales: Frye, Michaela, Bornelöv, Susanne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097682/
https://www.ncbi.nlm.nih.gov/pubmed/32866237
http://dx.doi.org/10.1093/bioinformatics/btaa733
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author Frye, Michaela
Bornelöv, Susanne
author_facet Frye, Michaela
Bornelöv, Susanne
author_sort Frye, Michaela
collection PubMed
description SUMMARY: CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. AVAILABILITY AND IMPLEMENTATION: CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-80976822021-05-10 CONCUR: quick and robust calculation of codon usage from ribosome profiling data Frye, Michaela Bornelöv, Susanne Bioinformatics Applications Notes SUMMARY: CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. AVAILABILITY AND IMPLEMENTATION: CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-08-31 /pmc/articles/PMC8097682/ /pubmed/32866237 http://dx.doi.org/10.1093/bioinformatics/btaa733 Text en © The Author(s) 2020. 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 (http://creativecommons.org/licenses/by/4.0/ (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 Notes
Frye, Michaela
Bornelöv, Susanne
CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title_full CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title_fullStr CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title_full_unstemmed CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title_short CONCUR: quick and robust calculation of codon usage from ribosome profiling data
title_sort concur: quick and robust calculation of codon usage from ribosome profiling data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097682/
https://www.ncbi.nlm.nih.gov/pubmed/32866237
http://dx.doi.org/10.1093/bioinformatics/btaa733
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