ArticleBMC genomics2018
PGAP-X: extension on pan-genome analysis pipeline.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
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- Next-Generation Breeding Strategies for Climate-Ready Crops.Frontiers in plant science · 2021Review
- Estimating Pangenomes with Roary.Molecular biology and evolution · 2020Article
- PRAP: Pan Resistome analysis pipeline.BMC bioinformatics · 2020Article
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- Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections.Microorganisms · 2019Article
- Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics.Frontiers in genetics · 2019Article
- A bioinformatics potpourri.BMC genomics · 2018Article
- PGAweb: A Web Server for Bacterial Pan-Genome Analysis.Frontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSince PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge.
resultTo well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process.
conclusionBriefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.