LRRprofiler is an automated program to detect and annotate LRR (Leucine-Rich Repeat) containing plant receptors.
Please cite : A New Comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice. Gottin C., Diévart A., Summo M., Droc G., Périn C., Ranwez V. and Chantret N. preprint on bioRxiv. doi: https://doi.org/10.1101/2021.01.29.428842
The program was developed on Linux os.
The program uses several external tools and databases:
- iTAK (v1.7)
- HMMER (v3.1b2)
- MAFFT (v7.271)
- TMHMM (v2.0c) [academic use only]
- SMART database
A singularity container for the LRRprofiler program can be download directly in your workspace with:
singularity pull LRRprofiler.sif library://cgottin/default/lrr_profiler:0.2
or from the Sylabs cloud .
The file LRRprofiler_v0.2_sing_3.6.def provide the corresponding singularity recipe.
The program can be run with the command line :
singularity run lrr_profiler0.1.sif --in_proteome <fastafile> --name <jobname> [--dev] [--nobuild]
Using the example file :
singularity run lrr_profiler0.1.sif --in_proteome Arabidopsis_Thaliana_reviewed_proteom_SwissProt_05-2020.fasta --name ARATH
--in_proteome: (mandatory) Path of the proteome fasta file. Currently, the program will work if all sequence headers are parsed without description (i.e. ">OS01g10200" and not ">OS01g10200 expressed protein")
--name: (mandatory) Character string used for output directory and file names.
--dev: (optional) If provided, the pipeline will retain the working directory containing temporary files.
--nobuild: (optional) If porvided, skip the profile refinement process and use exclusively profiles from the HMM_lib folder. This option can be useful to obtain homogeneous and reproductible annotation when comparing several proteomes.