Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKapitelVetenskapligPeer review

Sammanfattning

Analysis of gene families and identification of homologous genes are important for phylogenetic analysis
and for translating results from model to crop species. While numerous plant genomes have been sequenced
and made available, the identification of gene models can be difficult, in particular for large gene families
arranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correct
annotation of plant receptor kinases (PRK) is a challenge. Here, we describe a workflow for the semi-­
manual extraction, annotation, and verification of genes from annotated gene models as well as from
non-­annotated DNA regions. This protocol allows the efficient identification of gene family member of
PRK from most available plant genomes.
Originalspråkengelska
Titel på gästpublikationPlant Receptor Kinases : Methods and Protocols
RedaktörerReidunn Aalen
Antal sidor79
UtgivningsortNew York
FörlagSpringer
Utgivningsdatum2017
Sidor79-91
ISBN (tryckt)978-1-4939-7062-9
ISBN (elektroniskt)978-1-4939-7063-6
DOI
StatusPublicerad - 2017
MoE-publikationstypA3 Del av bok eller annan forskningsbok

Publikationsserier

NamnMethods in Molecular Biology
Nummer1621
ISSN (tryckt)1064-3745
ISSN (elektroniskt)1940-6029

Vetenskapsgrenar

  • 1183 Växtbiologi, mikrobiologi, virologi

Citera det här

Vaattovaara, A. F. M., Salojärvi, J. T., & Wrzaczek, M. A. (2017). Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. I R. Aalen (Red.), Plant Receptor Kinases : Methods and Protocols (s. 79-91). (Methods in Molecular Biology; Nr. 1621). New York: Springer. https://doi.org/10.1007/978-1-4939-7063-6_8
Vaattovaara, Aleksia Fanni Maria ; Salojärvi, Jarkko Tapani ; Wrzaczek, Michael Alois. / Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. Plant Receptor Kinases : Methods and Protocols. redaktör / Reidunn Aalen. New York : Springer, 2017. s. 79-91 (Methods in Molecular Biology; 1621).
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abstract = "Analysis of gene families and identification of homologous genes are important for phylogenetic analysisand for translating results from model to crop species. While numerous plant genomes have been sequencedand made available, the identification of gene models can be difficult, in particular for large gene familiesarranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correctannotation of plant receptor kinases (PRK) is a challenge. Here, we describe a workflow for the semi-­manual extraction, annotation, and verification of genes from annotated gene models as well as fromnon-­annotated DNA regions. This protocol allows the efficient identification of gene family member ofPRK from most available plant genomes.",
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Vaattovaara, AFM, Salojärvi, JT & Wrzaczek, MA 2017, Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. i R Aalen (red.), Plant Receptor Kinases : Methods and Protocols. Methods in Molecular Biology, nr. 1621, Springer, New York, s. 79-91. https://doi.org/10.1007/978-1-4939-7063-6_8

Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. / Vaattovaara, Aleksia Fanni Maria; Salojärvi, Jarkko Tapani; Wrzaczek, Michael Alois.

Plant Receptor Kinases : Methods and Protocols. red. / Reidunn Aalen. New York : Springer, 2017. s. 79-91 (Methods in Molecular Biology; Nr. 1621).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKapitelVetenskapligPeer review

TY - CHAP

T1 - Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis

AU - Vaattovaara, Aleksia Fanni Maria

AU - Salojärvi, Jarkko Tapani

AU - Wrzaczek, Michael Alois

PY - 2017

Y1 - 2017

N2 - Analysis of gene families and identification of homologous genes are important for phylogenetic analysisand for translating results from model to crop species. While numerous plant genomes have been sequencedand made available, the identification of gene models can be difficult, in particular for large gene familiesarranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correctannotation of plant receptor kinases (PRK) is a challenge. Here, we describe a workflow for the semi-­manual extraction, annotation, and verification of genes from annotated gene models as well as fromnon-­annotated DNA regions. This protocol allows the efficient identification of gene family member ofPRK from most available plant genomes.

AB - Analysis of gene families and identification of homologous genes are important for phylogenetic analysisand for translating results from model to crop species. While numerous plant genomes have been sequencedand made available, the identification of gene models can be difficult, in particular for large gene familiesarranged in tandem repeats or encoding proteins with a variable number of internal repeats. Thus, correctannotation of plant receptor kinases (PRK) is a challenge. Here, we describe a workflow for the semi-­manual extraction, annotation, and verification of genes from annotated gene models as well as fromnon-­annotated DNA regions. This protocol allows the efficient identification of gene family member ofPRK from most available plant genomes.

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Vaattovaara AFM, Salojärvi JT, Wrzaczek MA. Extraction and Curation of Gene Models for Plant Receptor Kinases for Phylogenetic Analysis. I Aalen R, redaktör, Plant Receptor Kinases : Methods and Protocols. New York: Springer. 2017. s. 79-91. (Methods in Molecular Biology; 1621). https://doi.org/10.1007/978-1-4939-7063-6_8