NLR-parser: rapid annotation of plant NLR complements.
Bioinformatics
; 31(10): 1665-7, 2015 May 15.
Article
em En
| MEDLINE
| ID: mdl-25586514
ABSTRACT
MOTIVATION The repetitive nature of plant disease resistance genes encoding for nucleotide-binding leucine-rich repeat (NLR) proteins hampers their prediction with standard gene annotation software. Motif alignment and search tool (MAST) has previously been reported as a tool to support annotation of NLR-encoding genes. However, the decision if a motif combination represents an NLR protein was entirely manual. RESULTS:
The NLR-parser pipeline is designed to use the MAST output from six-frame translated amino acid sequences and filters for predefined biologically curated motif compositions. Input reads can be derived from, for example, raw long-read sequencing data or contigs and scaffolds coming from plant genome projects. The output is a tab-separated file with information on start and frame of the first NLR specific motif, whether the identified sequence is a TNL or CNL, potentially full or fragmented. In addition, the output of the NB-ARC domain sequence can directly be used for phylogenetic analyses. In comparison to other prediction software, the highly complex NB-ARC domain is described in detail using several individual motifs.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Doenças das Plantas
/
Proteínas
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Análise de Sequência de DNA
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Arabidopsis
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Proteínas de Arabidopsis
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Anotação de Sequência Molecular
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Imunidade Inata
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article