qsap

name	qsap
description	QSAP — quorum-sensing (QS) related gene annotation pipeline against the QSP database (DIAMOND and/or HMMER). Use when mining autoinducer / QS circuitry (AHL, AIP, AI-2-related families as covered by QSP) from proteins or assemblies. Upstream: https://github.com/chunxiao-dcx/QSAP (QSP DB: https://github.com/chunxiao-dcx/QSP). Route via microbial-mining. Related secondary metabolites → antismash; Fe siderophores → fegenie.
license	MIT
category	analysis-tools
tags	["QSAP","quorum-sensing","QS","autoinducer","signaling","genome-mining"]
upstream	https://github.com/chunxiao-dcx/QSAP
stage	mining

QSAP (quorum sensing)

Upstream: chunxiao-dcx/QSAP · QSP database: https://github.com/chunxiao-dcx/QSP

Citation

Pipeline/DB: Dai, C. QSAP / QSP — quorum-sensing protein resources (https://github.com/chunxiao-dcx/QSAP). Cite the upstream repository and QSP release used; add peer-reviewed QSP/QSAP citation when available in Methods.

See also docs/references.md.

Analytical thinking

Quorum sensing (群体感应) coordinates population behaviors via signal synthases/receptors/transporters. QSAP classifies QS-related sequences from the QSP collection. Treat hits as genetic potential — not measured autoinducer concentrations.

Related claim	Prefer
QS genes	qsap
Specialized metabolite / AHL-adjacent BGCs	antismash
Siderophores (Fe acquisition signals/competition)	fegenie
Broad metabolism	dram / element-cycling

How to run

# install deps per QSAP README; example pattern
perl QSAP.pl -i input.list -o qsap_out -s sub -n 8
# strategies: diamond / hmmscan / sub|union — follow upstream help

Decision tree

Cell–cell signaling / QS?
├─ QS gene annotation → qsap
├─ BGC / natural products → antismash
├─ Siderophores → fegenie
└─ Plasmid-borne QS context → genomad / mob-suite ∩ qsap

Related skills

antismash · fegenie · dram · genomad · mob-suite · microbial-mining · tool-selection