Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups

Abstract Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred pr...

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Autores principales:	Andreas J. Stroehlein, Neil D. Young, Robin B. Gasser
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/38c0c09db0b64f58b536f456d9ea4d1e
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spelling	oai:doaj.org-article:38c0c09db0b64f58b536f456d9ea4d1e2021-12-02T11:40:26ZImproved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups10.1038/s41598-018-25020-82045-2322https://doaj.org/article/38c0c09db0b64f58b536f456d9ea4d1e2018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25020-8https://doaj.org/toc/2045-2322Abstract Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.Andreas J. StroehleinNeil D. YoungRobin B. GasserNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-10 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andreas J. Stroehlein Neil D. Young Robin B. Gasser Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
description	Abstract Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.
format	article
author	Andreas J. Stroehlein Neil D. Young Robin B. Gasser
author_facet	Andreas J. Stroehlein Neil D. Young Robin B. Gasser
author_sort	Andreas J. Stroehlein
title	Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
title_short	Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
title_full	Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
title_fullStr	Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
title_full_unstemmed	Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
title_sort	improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/38c0c09db0b64f58b536f456d9ea4d1e
work_keys_str_mv	AT andreasjstroehlein improvedstrategyforthecurationandclassificationofkinaseswithbroadapplicabilitytoothereukaryoticproteingroups AT neildyoung improvedstrategyforthecurationandclassificationofkinaseswithbroadapplicabilitytoothereukaryoticproteingroups AT robinbgasser improvedstrategyforthecurationandclassificationofkinaseswithbroadapplicabilitytoothereukaryoticproteingroups
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Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups

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