README.md

Mapping IDs to KEGG pathways

This pipeline uses following programs

• KEGG database
• BLAST software suite
• HMMER software suite
• Bedtools toolset
• NLRparser tools (including meme)

The basic steps in the pipeline are following

executed by run_bbh.sh

0. Prepare all data files, including NLR database.
1. Subtract genes with canonical NLR domains from a plant proteome(s) of interest.
2. Run blast of a plant proteome(s) against NLRs.
3. Intersect canonical NLR domains with blast results to filter them out.
4. Run the reciprocal blast.
5. Map reciprocal blast hits to KEGG pathways.

re-format results into human readable format with K-reformat-bbp-table.pl