DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation
As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics stu...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-04-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/full |
| _version_ | 1828280543160041472 |
|---|---|
| author | Rui Gan FengXia Zhou Yu Si Han Yang Chuangeng Chen Chunyan Ren Jiqiu Wu Fan Zhang |
| author_facet | Rui Gan FengXia Zhou Yu Si Han Yang Chuangeng Chen Chunyan Ren Jiqiu Wu Fan Zhang |
| author_sort | Rui Gan |
| collection | DOAJ |
| description | As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/. |
| first_indexed | 2024-04-13T08:00:09Z |
| format | Article |
| id | doaj.art-8672e195116b492087ea3dbfcab9e24b |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T08:00:09Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-8672e195116b492087ea3dbfcab9e24b2022-12-22T02:55:17ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-04-011310.3389/fgene.2022.885048885048DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and AnnotationRui Gan0FengXia Zhou1Yu Si2Han Yang3Chuangeng Chen4Chunyan Ren5Jiqiu Wu6Fan Zhang7HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaHIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaHIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaHIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaHIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaDepartment of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United StatesAPC Microbiome Ireland, School of Microbiology, University College Cork, Cork, IrelandHIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, ChinaAs an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/fullprophagephagedensity-based spatial clusteringsliding windowphage-host interaction |
| spellingShingle | Rui Gan FengXia Zhou Yu Si Han Yang Chuangeng Chen Chunyan Ren Jiqiu Wu Fan Zhang DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation Frontiers in Genetics prophage phage density-based spatial clustering sliding window phage-host interaction |
| title | DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation |
| title_full | DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation |
| title_fullStr | DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation |
| title_full_unstemmed | DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation |
| title_short | DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation |
| title_sort | dbscan swa an integrated tool for rapid prophage detection and annotation |
| topic | prophage phage density-based spatial clustering sliding window phage-host interaction |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/full |
| work_keys_str_mv | AT ruigan dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT fengxiazhou dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT yusi dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT hanyang dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT chuangengchen dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT chunyanren dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT jiqiuwu dbscanswaanintegratedtoolforrapidprophagedetectionandannotation AT fanzhang dbscanswaanintegratedtoolforrapidprophagedetectionandannotation |