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Bioinformatics. 2015 May 15;31(10):1665-7. doi: 10.1093/bioinformatics/btv005. Epub 2015 Jan 12.

NLR-parser: rapid annotation of plant NLR complements.

Author information

1
Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.

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.

PMID:
25586514
PMCID:
PMC4426836
DOI:
10.1093/bioinformatics/btv005
[Indexed for MEDLINE]
Free PMC Article

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