IPGA: A handy integrated prokaryotes genome and pan‐genome analysis web service. Issue 4 (14th September 2022)

• Record Type: Journal Article
• Authors: Liu, Dongmei; Zhang, Yifei; Fan, Guomei; Sun, Dingzhong; Zhang, Xingjiao; Yu, Zhengfei; Wang, Jinfeng; Wu, Linhuan; Shi, Wenyu; Ma, Juncai
• Is Part Of: IMeta. Volume 1:Issue 4(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-09-14
• Subjects: comparative genomics -- pan‐genome -- web service; Metagenomics -- Periodicals; Bioinformatics -- Periodicals; Bioinformatics; Metagenomics; Metagenomics; Metagenome; Computational Biology; Periodicals; Periodical; 576.5
• DOI: 10.1002/imt2.55
• Languages: English
• ISSNs: 2770-596X

Abstract

Abstract: Pan‐genomics is one of the most powerful means to study genomic variation and obtain a sketch of genes within a defined clade of species. Though there are a lot of computational tools to achieve this, an integrated framework to evaluate their performance and offer the best choice to users has never been achieved. To ease the process of large‐scale prokaryotic genome analysis, we introduce Integrated Prokaryotes Genome and pan‐genome Analysis (IPGA), a one‐stop web service to analyze, compare, and visualize pan‐genome as well as individual genomes, that rids users of installing any specific tools. IPGA features a scoring system that helps users to evaluate the reliability of pan‐genome profiles generated by different packages. Thus, IPGA can help users ascertain the profiling method that is most suitable for their data set for the following analysis. In addition, IPGA integrates several downstream comparative analysis and genome analysis modules to make users achieve diverse targets. Abstract : Integrated Prokaryotes Genome and pan‐genome Analysis (IPGA) serves as a free and easy‐to‐use web‐based system that could provide up‐to‐date pan‐genome analysis service for non‐bioinformaticians. IPGA offers users the most reliable pan‐genome profile which enables users to perform additional comparative genomic analysis. IPGA provides a series of downstream analysis modules such as phylogenetic inference, synteny inference, and target genome annotation. Highlights: IPGA serves as a free and easy‐to‐use web‐based system that could provide up‐to‐date pan‐genome analysis service for non‐bioinformaticians. IPGA offers users the most reliable pan‐genome profile which enables users to perform additional comparative genomic analysis. IPGA provides a series of downstream analysis modules such as phylogenetic inference, synteny inference, and target genome annotation.