title: NLR-parser: rapid annotation of plant NLR complements.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.
authors.forename: Florian
authors.initials: F
authors.lastname: Jupe
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.
authors.forename: Kamil
authors.initials: K
authors.lastname: Witek
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.
authors.forename: Jonathan D G
authors.initials: JD
authors.lastname: Jones
authors.affiliation: Department of Crop Genetics, John Innes Centre, Norwich, UK and The Sainsbury Laboratory, Norwich, UK.
authors.forename: Brande B H
authors.initials: BB
authors.lastname: Wulff
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D007113:Immunity, Innate / Q000235:genetics*; D000090263:Leucine-Rich Repeat Proteins; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology; D011506:Proteins / Q000235:genetics*; D020449:Repetitive Sequences, Amino Acid / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D029681:Arabidopsis Proteins; D000090263:Leucine-Rich Repeat Proteins; D011506:Proteins