Have you wondered what the settings for HHPred, NCBI-blastp, and CDD are used by PECAAN?
The parameters that we run for HHPred are as follows:
Hhsuitedb: "mmcif70/pdb70 NCBI_CD/NCBI_CD scope70/scope70 pfama/pfama",
Proteomes: "",
MsaGenMethod: "UniRef30",
MsaGenMaxIter: "3",
HhpredInclEval: "1e-3",
MinSeqidQuery: "0",
MinCov: "20",
SSScoring: "2",
AlignMacMode: "loc",
MacThreshold: "0.3",
Desc: "250",
Pmin: "20",

and
Blastp from ncbi blast 2.13.0+ is ran remotely with
-db nr
-gapopen 11
-gapextend 1
-word_size 6
-threshold 21
-window_size 40
-evalue 0.05
-max_target_seqs 100
-outfmt 5
-remote
and
The CDD database is searched by rpsblast from ncbi blast 2.13.0+ with the following arguments

-num_alignments=50
-evalue 0.01

7/7/2022
Edited 07 Jul, 2022 23:48