SUSSscan

Scan fungal proteome FASTA for identifiable effectors and predicted SUSS structural families based on RemEff clusters from the publication below:

Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi
DAB Jones, PM Moolhuijzen, JK Hane
Microbial Genomics 7 (9), 000637
https://doi.org/10.6084/m9.figshare.32859416

Outputs: CSV and GFF3

SUSSscan.py enables rapid identification of known effectors and prediction of SUSS (sequence-unrelated structurally-similar) effector families, for further validation with more cpu-intensive structural bioinformatic methods. The RemEff dataset contains 3 levels of protein clusters containing at least 1 known effector. Level 1 = proteins clustered on similar sequence. Level 2 = HMM-HMM clusters. Level 3 = combination of Hidden-Markov, Greedy and Connected Component clusters of similar level 2 clusters. SUSSscan adds Level 4 descriptive groupings of SUSS families.

Details of SUSS Level 4 groupings are contained in data/SUSS.csv Details of selected Pfam and publication-derived HMM models relevant to known effectors are in data/Other.csv

Installation

Clone the repository:

git clone https://github.com/ccdmb/SUSSscan.git
cd SUSSscan

run install.sh to download Remeff and Other (selected Pfam and publication-derived HMM) databases from https://doi.org/10.6084/m9.figshare.32859416

Basic Scan (All Hits):

python SUSSscan.py -i input_proteins.fasta -o output_results.tsv

Filter to Top 5 Hits Per Sequence:

python SUSSscan.py -i input_proteins.fasta -o output_results.tsv --top-hits 5

Run using multiple CPU threads for speed:

python SUSSscan.py -i input_proteins.fasta -o output_results.tsv --threads 8

Usage:

usage: SUSSscan.py [-h] -i INPUT -o OUTPUT [-d DATABASE] [--other-database OTHER_DATABASE] [-c CSV]
                   [--other-csv OTHER_CSV] [-e EVALUE] [--keep-tblout] [--hmmsearch HMMSEARCH] [--cpu CPU]
                   [--top-hits TOP_HITS]

SUSSscan: Search protein sequences against SUSS/Remeff database and annotate hits.

options:
  -h, --help            show this help message and exit
  -i, --input INPUT     Input protein FASTA file
  -o, --output OUTPUT   Output annotated CSV file
  -d, --database DATABASE
                        SUSS/Remeff hmmsearch database file, prefix, or glob pattern (default: data/Remeff.*.hmm)
  --other-database OTHER_DATABASE
                        Other hmmsearch database file, prefix, or glob pattern (default: data/Other.*.hmm)
  -c, --csv CSV         SUSS reference CSV (default: data/SUSS.csv)
  --other-csv OTHER_CSV
                        Other reference CSV (default: data/Other.csv)
  -e, --evalue EVALUE   E-value cutoff (default: 1e-3)
  --keep-tblout         Keep the intermediate .domtblout file
  --hmmsearch HMMSEARCH
                        Path to hmmsearch executable if not in PATH
  --cpu CPU             Number of CPUs to use for hmmsearch (default: all available CPUs)
  --top-hits TOP_HITS   Only output up to the top N hits per query sequence. Use 0 or negative to output all hits