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GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences
BACKGROUND: Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate sh...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372895/ https://www.ncbi.nlm.nih.gov/pubmed/32690023 http://dx.doi.org/10.1186/s12859-020-03657-5 |
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author | Gabrielaite, Migle Marvig, Rasmus L. |
author_facet | Gabrielaite, Migle Marvig, Rasmus L. |
author_sort | Gabrielaite, Migle |
collection | PubMed |
description | BACKGROUND: Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate short genome sequence reads to disentangle phenotypic changes caused by gene loss and acquisition, the short-read genome sequencing often results in fragmented genome assemblies as a basis for identification of gene loss and acquisition events. However, sensitive and precise determination of gene content change for fragmented genome assemblies remains challenging as analysis needs to account for cases when only a fragment of the gene is assembled or when the gene assembly is split in more than one contig. RESULTS: We developed GenAPI, a command-line tool that is designed to compare the gene content of bacterial genomes for which only fragmented genome assemblies are available. GenAPI, unlike other available tools of similar purpose, accounts for imperfections in sequencing and assembly, and aims to compensate for them. We tested the performance of GenAPI on three different datasets to show that GenAPI has a high sensitivity while it maintains precision when dealing with partly assembled genes in both simulated and real datasets. Furthermore, we benchmarked the performance of GenAPI with six popular tools for gene presence-absence identification. CONCLUSIONS: Our developed bioinformatics tool, called GenAPI, has the same precision and recall rates when analyzing complete genome sequences as the other tools of the same purpose; however, GenAPI’s performance is markedly better on fragmented genome assemblies. |
format | Online Article Text |
id | pubmed-7372895 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-73728952020-07-21 GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences Gabrielaite, Migle Marvig, Rasmus L. BMC Bioinformatics Software BACKGROUND: Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate short genome sequence reads to disentangle phenotypic changes caused by gene loss and acquisition, the short-read genome sequencing often results in fragmented genome assemblies as a basis for identification of gene loss and acquisition events. However, sensitive and precise determination of gene content change for fragmented genome assemblies remains challenging as analysis needs to account for cases when only a fragment of the gene is assembled or when the gene assembly is split in more than one contig. RESULTS: We developed GenAPI, a command-line tool that is designed to compare the gene content of bacterial genomes for which only fragmented genome assemblies are available. GenAPI, unlike other available tools of similar purpose, accounts for imperfections in sequencing and assembly, and aims to compensate for them. We tested the performance of GenAPI on three different datasets to show that GenAPI has a high sensitivity while it maintains precision when dealing with partly assembled genes in both simulated and real datasets. Furthermore, we benchmarked the performance of GenAPI with six popular tools for gene presence-absence identification. CONCLUSIONS: Our developed bioinformatics tool, called GenAPI, has the same precision and recall rates when analyzing complete genome sequences as the other tools of the same purpose; however, GenAPI’s performance is markedly better on fragmented genome assemblies. BioMed Central 2020-07-20 /pmc/articles/PMC7372895/ /pubmed/32690023 http://dx.doi.org/10.1186/s12859-020-03657-5 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Gabrielaite, Migle Marvig, Rasmus L. GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title | GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title_full | GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title_fullStr | GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title_full_unstemmed | GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title_short | GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
title_sort | genapi: a tool for gene absence-presence identification in fragmented bacterial genome sequences |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372895/ https://www.ncbi.nlm.nih.gov/pubmed/32690023 http://dx.doi.org/10.1186/s12859-020-03657-5 |
work_keys_str_mv | AT gabrielaitemigle genapiatoolforgeneabsencepresenceidentificationinfragmentedbacterialgenomesequences AT marvigrasmusl genapiatoolforgeneabsencepresenceidentificationinfragmentedbacterialgenomesequences |