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] -iINPUT-oOUTPUT [-dDATABASE] [--other-databaseOTHER_DATABASE] [-cCSV]
[--other-csvOTHER_CSV] [-eEVALUE] [--keep-tblout] [--hmmsearchHMMSEARCH] [--cpuCPU]
[--top-hitsTOP_HITS]
SUSSscan: SearchproteinsequencesagainstSUSS/Remeffdatabaseandannotatehits.
options:
-h, --helpshowthishelpmessageandexit-i, --inputINPUTInputproteinFASTAfile-o, --outputOUTPUTOutputannotatedCSVfile-d, --databaseDATABASESUSS/Remeffhmmsearchdatabasefile, prefix, orglobpattern (default: data/Remeff.*.hmm)
--other-databaseOTHER_DATABASEOtherhmmsearchdatabasefile, prefix, orglobpattern (default: data/Other.*.hmm)
-c, --csvCSVSUSSreferenceCSV (default: data/SUSS.csv)
--other-csvOTHER_CSVOtherreferenceCSV (default: data/Other.csv)
-e, --evalueEVALUEE-valuecutoff (default: 1e-3)
--keep-tbloutKeeptheintermediate .domtbloutfile--hmmsearchHMMSEARCHPathtohmmsearchexecutableifnotinPATH--cpuCPUNumberofCPUstouseforhmmsearch (default: allavailableCPUs)
--top-hitsTOP_HITSOnlyoutputuptothetopNhitsperquerysequence. Use0ornegativetooutputallhits