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A Brief Review of Software Tools for Pangenomics

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific p...

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Detalles Bibliográficos
Autores principales: Xiao, Jingfa, Zhang, Zhewen, Wu, Jiayan, Yu, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411478/
https://www.ncbi.nlm.nih.gov/pubmed/25721608
http://dx.doi.org/10.1016/j.gpb.2015.01.007
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author Xiao, Jingfa
Zhang, Zhewen
Wu, Jiayan
Yu, Jun
author_facet Xiao, Jingfa
Zhang, Zhewen
Wu, Jiayan
Yu, Jun
author_sort Xiao, Jingfa
collection PubMed
description Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
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spelling pubmed-44114782015-05-06 A Brief Review of Software Tools for Pangenomics Xiao, Jingfa Zhang, Zhewen Wu, Jiayan Yu, Jun Genomics Proteomics Bioinformatics Resource Review Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence. Elsevier 2015-02 2015-02-23 /pmc/articles/PMC4411478/ /pubmed/25721608 http://dx.doi.org/10.1016/j.gpb.2015.01.007 Text en © 2015 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Resource Review
Xiao, Jingfa
Zhang, Zhewen
Wu, Jiayan
Yu, Jun
A Brief Review of Software Tools for Pangenomics
title A Brief Review of Software Tools for Pangenomics
title_full A Brief Review of Software Tools for Pangenomics
title_fullStr A Brief Review of Software Tools for Pangenomics
title_full_unstemmed A Brief Review of Software Tools for Pangenomics
title_short A Brief Review of Software Tools for Pangenomics
title_sort brief review of software tools for pangenomics
topic Resource Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411478/
https://www.ncbi.nlm.nih.gov/pubmed/25721608
http://dx.doi.org/10.1016/j.gpb.2015.01.007
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