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iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies

We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate sy...

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Detalles Bibliográficos
Autores principales: Standage, Daniel S, Lai, Tim, Brendel, Volker P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862717/
https://www.ncbi.nlm.nih.gov/pubmed/35211671
http://dx.doi.org/10.1093/nargab/lqac013
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author Standage, Daniel S
Lai, Tim
Brendel, Volker P
author_facet Standage, Daniel S
Lai, Tim
Brendel, Volker P
author_sort Standage, Daniel S
collection PubMed
description We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide characteristics of gene arrangements in the whole genome context. Given the fast pace of assembly/annotation updates, our AEGeAn Toolkit fills a niche in computational genomics based on deriving persistent and species-specific genome statistics. Gene structure model-centric iLoci provide a precisely defined coordinate system that can be used to store assembly/annotation updates that reflect either stable or changed assessments. Large-scale application of the approach revealed species- and clade-specific genome organization in precisely defined computational terms, promising intriguing forays into the forces of shaping genome structure as more and more genome assemblies are being deposited.
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spelling pubmed-88627172022-02-23 iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies Standage, Daniel S Lai, Tim Brendel, Volker P NAR Genom Bioinform High Throughput Sequencing Methods We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide characteristics of gene arrangements in the whole genome context. Given the fast pace of assembly/annotation updates, our AEGeAn Toolkit fills a niche in computational genomics based on deriving persistent and species-specific genome statistics. Gene structure model-centric iLoci provide a precisely defined coordinate system that can be used to store assembly/annotation updates that reflect either stable or changed assessments. Large-scale application of the approach revealed species- and clade-specific genome organization in precisely defined computational terms, promising intriguing forays into the forces of shaping genome structure as more and more genome assemblies are being deposited. Oxford University Press 2022-02-22 /pmc/articles/PMC8862717/ /pubmed/35211671 http://dx.doi.org/10.1093/nargab/lqac013 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle High Throughput Sequencing Methods
Standage, Daniel S
Lai, Tim
Brendel, Volker P
iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title_full iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title_fullStr iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title_full_unstemmed iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title_short iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies
title_sort iloci: robust evaluation of genome content and organization for provisional and mature genome assemblies
topic High Throughput Sequencing Methods
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8862717/
https://www.ncbi.nlm.nih.gov/pubmed/35211671
http://dx.doi.org/10.1093/nargab/lqac013
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