PGAP pipeline

PGAP specifications

Information


Unique identifier OMICS_10860
Name PGAP
Alternative name Prokaryotic Genome Annotation Pipeline
Interface Web user interface
Restrictions to use None
Input data On input, PGAP accepts an assembly (either draft or complete) with a predefined NCBI Taxonomy ID that defines the genetic code of the organism. PGAP also accepts a predetermined clade identifier, matching the genome in question to a species-specific clade.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mark Borodovsky <>

Publications for Prokaryotic Genome Annotation Pipeline

PGAP IN pipelines

 (54)
2018
PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17

[…] final scaffolds included 12 contigs with a combined total of 2,773,925 bp and a g+c content of 32.71%. the n50 value for the genome was 444,128 bp. a total of 2,860 genes were predicted by the ncbi prokaryotic genome annotation pipeline (14)., the draft genome sequence of strain 209 was deposited at ddbj/ena/genbank under the accession number ntcy00000000., citation chen y, crosby ha, […]

2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] a final scaffolding step was performed using sspace (12). final draft genome completeness and contamination was assessed using checkm (13). the final draft genome was annotated using the ncbi prokaryotic genome annotation pipeline (pgap) (14) and reviewed using rast v2.0 (15)., this resulted in a 3.47-mbp draft genome estimated to be 93.9% complete with 1.79% potential contamination, […]

2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] genome coverage. these reads were assembled in newbler 2.8 software (roche), and gaps were closed by local assembly of selected reads in staden software [29] into a single circular contig., the ncbi prokaryotic genome annotation pipeline [30] was used for automated genome annotation, and functional annotations were carried out by searching against kegg [31], cog [32] and pfam [33] databases. […]

2018
PMCID: 5834334
PMID: 29496837
DOI: 10.1128/genomeA.00119-18

[…] 0104j (genbank accession number am946015) by progressivemauve alignment (10). genomic features and coding dna sequences (cdss) were predicted with the ncbi prokaryote genome annotation pipeline (pgap) (11)., the complete nz01 genome comprises a single chromosome of 1,863,842 bp, with 1,808 cdss and 1,886 predicted genes. approximately 146 cdss found in the nz01 genome are novel, compared […]

2018
PMCID: 5897803
PMID: 29650582
DOI: 10.1128/genomeA.00290-18

[…] of the reference s. pseudintermedius strain 081661 (genbank accession no. nzcp016073) (23) using progressivemauve (24). automated annotation of the assembled contigs was performed using the ncbi prokaryotic genome annotation pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). whole-genome multilocus sequence typing was performed using the staphylococcus pseudintermedius mlst […]

PGAP institution(s)
National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, GA, USA; School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, USA
PGAP funding source(s)
Intramural Research Program of the NIH National Library of Medicine (in part); NIH grant HG000783 (in part)

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