biostudies-literatureSteuernagel BBiotechnology and Biological Sciences Research Council1665-7https://www.ebi.ac.uk/biostudies/studies/S-EPMC4426836biostudies-literatureUnknown31(10)<h4>Motivation</h4>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.<h4>Results</h4>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 oBioinformatics (Oxford, England)NLR-parser: rapid annotation of plant NLR complements.PMC4426836BB/L009293/1BB/H019820/1BB/M003809/1BB/J003166/1BB/L011794/1Jones JDWulff BBSteuernagel BJupe FWitek KfalseNLR-parser: rapid annotation of plant NLR complements.<h4>Motivation</h4>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.<h4>Results</h4>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 o2015-01-01T00:00:00Z2015 May2026-04-29T07:43:40.242Z2026-04-07T15:03:33.147ZS-EPMC44268362558651410.1093/bioinformatics/btv005