PGAdb-builder protocols

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PGAdb-builder specifications

Information


Unique identifier OMICS_18161
Name PGAdb-builder
Interface Web user interface
Restrictions to use None
Input data Some genome contigs.
Input format FASTA
Programming languages PHP
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chih-Chieh Chen <>

Publication for PGAdb-builder

PGAdb-builder in pipeline

2017
PMCID: 5609107
PMID: 28970823
DOI: 10.3389/fmicb.2017.01790

[…] (huson, ). the equal angle method was used to construct the phylogenetic network, which was plotted with neighbornet., a wgmlst analysis was performed using the build_wgmlsttree module in the pgadb-builder web service tool (liu et al., ). the 17 genome sequences were compared with the resulting pgadb profile using blastn, with filters of 80% coverage and 90% identity., we also performed […]


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PGAdb-builder in publications

 (4)
PMCID: 5817063
PMID: 29491851
DOI: 10.3389/fmicb.2018.00184

[…] also investigated for secondary metabolite non-ribosomal peptide synthetase (nrps) biosynthesis gene clusters using the antismash bacterial server. whole genome mlst (wgmslt) was conducted using pgadb-builder (liu et al., ). the 95% occurrence allele scheme was selected to generate a wgmlst tree with p. agglomerans pc10 and p. stewartii subsp. indologens lmg 2632 selected as outgroups […]

PMCID: 5609107
PMID: 28970823
DOI: 10.3389/fmicb.2017.01790

[…] (huson, ). the equal angle method was used to construct the phylogenetic network, which was plotted with neighbornet., a wgmlst analysis was performed using the build_wgmlsttree module in the pgadb-builder web service tool (liu et al., ). the 17 genome sequences were compared with the resulting pgadb profile using blastn, with filters of 80% coverage and 90% identity., we also performed […]

PMCID: 5506229
PMID: 28747902
DOI: 10.3389/fmicb.2017.01296

[…] to refine their evolutionary relationships which unfortunately is beyond the scope of this study. such wgmlst analysis can be performed using existing bioinformatic tools such as bigsdb, roary and pgadb-builder (jolley and maiden, ; page et al., ; liu et al., ). strikingly, several whole genome sequences labeled as the same pseudomonas species were located in different major clades […]

PMCID: 5156723
PMID: 28018331
DOI: 10.3389/fmicb.2016.02010

[…] complete genomic sequences or genomic contigs were first annotated using prokka (), a rapid bacterial genome annotation pipeline, to generate output gff files. the gff files were processed using the pgadb_builder, a pipeline for construction of a bacterial pan-genome allele database (). in this study, paralogous genes were excluded from the dataset, and proteins sharing ≥95% amino acid sequence […]


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PGAdb-builder institution(s)
Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan; Medical Science and Technology Center, National Sun Yat-sen University, Kaohsiung, Taiwan
PGAdb-builder funding source(s)
Supported by grant from ‘Academic Summit Program’ of Ministry of Science and Technology (MOST-105-2221-E-110-079), ‘Medical Science and Technology Center of Aiming for the Top University Program’ of National Sun Yat-sen University and Ministry of Education, Taiwan, and also a grant (MOHW105- CDC-C-315-123301) from Centers for Disease Control, the Ministry of Health and Welfare, Taiwan.

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