NLR-parser

NLR-parser annotates nucleotide-binding leucine-rich repeat (NLR) proteins in plant genomes by filtering MAST six-frame translated amino acid sequence outputs for biologically curated motif compositions to support NLR classification and downstream analyses such as phylogenetics and comparative genomics.

Key Features:

• Automated annotation pipeline: Automates identification and annotation of NLR-encoding genes by leveraging outputs from the Motif Alignment and Search Tool (MAST).
• Integration with MAST outputs: Processes six-frame translated amino acid sequences generated by MAST to identify predefined biologically curated motif compositions associated with NLR proteins.
• Versatile input compatibility: Accepts raw long-read sequencing data and contigs/scaffolds from plant genome projects as input.
• Detailed tab-delimited output: Produces a tab-separated file that reports the start position and frame of the first NLR-specific motif, classification as TNL (TIR-NB-LRR) or CNL (CC-NB-LRR), and full-length or fragmented status.
• NB-ARC sequence extraction for phylogenetics: Provides sequences of the NB-ARC domain, represented by multiple individual motifs, for direct use in phylogenetic analyses.

Scientific Applications:

• Plant disease resistance studies: Enables precise annotation of NLR proteins to investigate molecular mechanisms of pathogen resistance in plants.
• Comparative genomics: Facilitates comparison of NLR repertoires across plant genomes using motif-based annotations.
• Evolutionary biology: Supports analyses of NLR domain architecture and motif composition in evolutionary studies.
• Phylogenetic analysis: Supplies NB-ARC domain sequences for construction of phylogenetic trees of NLRs.

Methodology:

Processes six-frame translated amino acid sequences from MAST and filters MAST outputs for biologically curated motif compositions, then outputs tab-separated annotation records and NB-ARC domain sequences.