{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T05:15:29Z","timestamp":1779167729801,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":628,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and implementation: The NLR-parser tool can be downloaded from Git-Hub (github.com\/steuernb\/NLR-Parser). It requires a valid Java installation as well as MAST as part of the MEME Suite. The tool is run from the command line.<\/jats:p>\n               <jats:p>Contact: \u00a0burkhard.steuernagel@jic.ac.uk; fjupe@salk.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv005","type":"journal-article","created":{"date-parts":[[2015,1,14]],"date-time":"2015-01-14T02:18:45Z","timestamp":1421201925000},"page":"1665-1667","source":"Crossref","is-referenced-by-count":115,"title":["NLR-parser: rapid annotation of plant NLR complements"],"prefix":"10.1093","volume":"31","author":[{"given":"Burkhard","family":"Steuernagel","sequence":"first","affiliation":[{"name":"1 Department of Crop Genetics, John Innes Centre, Norwich, UK and 2The Sainsbury Laboratory, Norwich, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Jupe","sequence":"additional","affiliation":[{"name":"1 Department of Crop Genetics, John Innes Centre, Norwich, UK and 2The Sainsbury Laboratory, Norwich, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamil","family":"Witek","sequence":"additional","affiliation":[{"name":"1 Department of Crop Genetics, John Innes Centre, Norwich, UK and 2The Sainsbury Laboratory, Norwich, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan D.G.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Department of Crop Genetics, John Innes Centre, Norwich, UK and 2The Sainsbury Laboratory, Norwich, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brande B.H.","family":"Wulff","sequence":"additional","affiliation":[{"name":"1 Department of Crop Genetics, John Innes Centre, Norwich, UK and 2The Sainsbury Laboratory, Norwich, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,1,12]]},"reference":[{"key":"2023020115461894300_btv005-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2229-14-120","article-title":"Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq","volume":"14","author":"Andolfo","year":"2014","journal-title":"BMC Plant Biol."},{"key":"2023020115461894300_btv005-B2","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020115461894300_btv005-B3","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1007\/s00425-005-1499-3","article-title":"Motifs specific for the ADR1 NBS-LRR protein family in Arabidopsis are conserved among NBS-LRR sequences from both dicotyledonous and monocotyledonous plants","volume":"221","author":"Chini","year":"2005","journal-title":"Planta"},{"key":"2023020115461894300_btv005-B4","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1126\/science.1236011","article-title":"Pivoting the plant immune system from dissection to deployment","volume":"341","author":"Dangl","year":"2013","journal-title":"Science"},{"key":"2023020115461894300_btv005-B5","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. 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