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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
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QSP: An open sequence database for quorum sensing related gene analysis with an automatic annotation pipeline
Chunxiao Dai1, Yuanyuan Qu1, Weize Wu1
1Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
Water Research
|March 19, 2023
Summary
Scientists created a database and pipeline for annotating bacterial quorum sensing (QS) sequences. This tool aids in understanding bacterial communication in aquatic environments and managing water resources effectively.
Area of Science:
- Microbiology
- Bioinformatics
- Environmental Science
Background:
- Quorum sensing (QS) is crucial for bacterial interactions and water management.
- High-throughput sequencing necessitates a dedicated database for QS-related sequence annotation.
Purpose of the Study:
- To develop a comprehensive database and an automated annotation pipeline for quorum sensing proteins.
- To facilitate the study of bacterial communication in aquatic ecosystems.
Main Methods:
- Built Hidden Markov Model (HMM) profiles for 38 types of QS proteins using 4024 seed sequences.
- Established a QS-related protein (QSP) database with 809,721 protein and 186,133 nucleotide sequences via homolog search and keyword confirmation.
- Developed the QSAP pipeline for rapid annotation, classification, and abundance quantification using Diamond or HMMER alignment strategies.
Main Results:
- The QSP database contains 809,721 protein and 186,133 nucleotide sequences, classified into 38 types and 315 subtypes across 91 bacterial phyla.
- The QSAP pipeline successfully annotated sequences from 14 diverse aquatic metagenomic samples.
- Both the database and pipeline are publicly available via GitHub.
Conclusions:
- The QSP database and QSAP pipeline provide essential tools for QS-related sequence annotation.
- These resources will enhance the understanding of QS communication in various aquatic environments.
- Facilitates research in bacterial interactions and water management applications.
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