daniel-ze / exnlrs

exNLRs.sh works with the results of NLR-parser

NLR-parser additional scripts: exNLRs.sh, plot-nlr.r, exSeqList.py

Description

The shell script exNLRs.sh was written around the java application NLR-parser.jar by Steuernagel et al., 2015 to automate the extraction of NLRs after prediction of proteins. The script takes in a multifasta file and runs NLR-parser over it. NLR-parser is run with standard settings (p-value 1E-5) and complete and partial NLRs are written to multifasta file plus the NB-Arc domain sequences are written in multifasta files from complete and partial NLRs. Additionally complete CNLs are scanned for the MADA motif using hammersearch and the mada.hmm file from Adachi et al., 2019.

Citing NLR-parser:

NLR-parser: Rapid annotation of plant NLR complements
Steuernagel, B., Jupe, F., Witek, K., Jones, J. D.G., Wulff, B. B.H.
Bioinformatics 2015
doi: 10.1093/bioinformatics/btv005

Identification and localisation of the NB-LRR gene family within the potato genome
Jupe, F., Pritchard, L., Etherington, G. J., MacKenzie, K., Cock, P. J.A., Wright, F., Sharma, S. K., Bolser, D., Bryan, G. J., Jones, J. D.G., Hein, I.
BMC Genomics 2012
doi: 10.1186/1471-2164-13-75

Citing MADA motif:

An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species Adachi, H., Contreras, M., Harant, A., Wu, C., Derevnina, L., Sakai, T., Duggan, C., Moratto, Eleonora, Bozkurt, T. O., Maqbool, A., Win, J., Kamoun, S. eLife 2019 doi: 10.7554/eLife.49956

Github page of NLR-parser:

https://github.com/steuernb/NLR-parser

What does the script do

1. make directory NLR in the same directory where the multi fasta file is located
2. call mast with the meme.xml file from NLR-parser
3. parse mast results with NLR-parser.jar
4. generate some stats about the amount of different NLRs identified with mast
5. plot the stats with plot-nlr.r
6. extract the complete and partial NLR sequence names and subsequently the corresponding sequence with exSeqList.py (exSeqList.py can extract any fasta sequence from any multifasta file: exSeqList.py seqNames multifasta.fa) plus NB-Arc domain multifata files with exNB.py.
7. extract the complete CNLs and search for MADA motif with hmmersearch; extrat CNLs with MADA motif and their NB-Arc domain
8. everythings saved in the directory NLR and stuff gets sorted in folders
9. all errors are printed to file exNLR.stderr

What does it depend on

Dependencies of this script:

• A running version of NLR-parser with mast v4.9.1
• Rscript
  • library: ggplot2
• python 2.7 or 3.6
  • python script exSeqList.py, exNB.py
• HMMER 3.2.1
• download MADA.hmm: https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNDk5NTYvZWxpZmUtNDk5NTYtc3VwcDItdjIuaG1t/elife-49956-supp2-v2.hmm?_hash=57ZnZsThc0bH7%2BYiqwC70b94%2F6PuiEzSL0QYmpp%2F4KM%3D
  • name the .hmm file mada.hmm
  • copy in NLR-parser directory

How to get it running

Get the script running:

• Install and download the dependencies
• Put all the scripts in the NLR-parser directory
• Put your NLR-parser directory in your path (edit .bash_profile):
  • export PATH="/path/to/NLR-parser:$PATH"
• edit line 6 in exNLRs.sh to fit the path to your NLR-parser.jar directory
• Make the file executable:
  • $ chmod a+x /usr/local/bin/exNLRs.sh
• Run the script:
  • $ exNLRs.sh /path/to/fasta/file.fa

Tested on MacOS and Ubuntu Linux.

exnlrs's Issues

Regarding NLR Annotator meme suite version issue.

Greetings,

I am having the same problem while installing older version of meme suite. I wonder how you resolved the issue as i saw your issue post on Burkhard's profile. Please guide me as the make command is showing some error most probably some bug in older version.
Sincerely,
Ankush Sharma