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Protocols

PGDB specifications

Information


Unique identifier OMICS_26818
Name PGDB
Alternative name Human Prostate Gene DataBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Rajvir Dahiya

Publication for Human Prostate Gene DataBase

PGDB citations

 (19)
library_books

Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium

2017
Front Microbiol
PMCID: 5702781
PMID: 29213256
DOI: 10.3389/fmicb.2017.02290

[…] construct the genome-scale metabolic models (GEM) of S. symbiotica SCc and B. aphidicola BCc, we retrieved the corresponding genomes and the semi-automatically reconstructed Pathway-Genome Databases (PGDB) available in the BioCyc collection in Caspi et al. (). The used PGDBs' versions were SSYM568817 19.0 for S. symbiotica SCc, and BAPH37261 19.0 for B. aphidicola BCc (both available in Tier 3 at […]

library_books

Analyses of the probiotic property and stress resistance related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays

2017
PLoS One
PMCID: 5383145
PMID: 28384209
DOI: 10.1371/journal.pone.0175116

[…] A genome sequence in.fasta and a genome annotation in the.gbk format were used for reconstructing the Lactococcus species metabolic pathways. Posteriorly, the Pathway/Genome Databases (PGDB) for each of the 16 strains were computationally predicted using Pathway Tools software version 16.5 [], developed by SRI International. The MetaCyc, a highly curated and non-redundant reference […]

library_books

Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication

2017
Genome Biol Evol
PMCID: 5381638
PMID: 28082605
DOI: 10.1093/gbe/evw292

[…] ns difficult, but several hypotheses can be proposed. First, several PBLEs seems to be potentially active, or at least they were within the recent past. Second, the general phylogeny, including PBLE, PGDB and PGDB-like, shows that a close relationship can be observed between PGBD and PBLE or PGBD-like. For instance, PvaPBLE of Pteropus vampyrus is closely related to the members of PGBD4. The PBLE […]

library_books

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

2016
Genome Biol
PMCID: 5034548
PMID: 27659211
DOI: 10.1186/s13059-016-1049-2

[…] pecies complex, though none have been shown to be functional [, ]. Indeed, amino acid sequences in the medfly database that are most highly similar to piggyBac transposase by BLASTp include the human Pgdb4 isoform X2 (1e–27; XP_012161257.1) and piggyBac-derived protein 4-like (1e–25; XP_004524835.1) sequences, all of which belong to the transposase IS4 family having the DDE_Tnp_1_7 domain. Alignme […]

call_split

Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

2016
PLoS One
PMCID: 4798299
PMID: 26992093
DOI: 10.1371/journal.pone.0150974
call_split See protocol

[…] atabase was performed using the PathoLogic algorithm in the Pathway Tools software version 19.0 []. Pathway Tools computationally reconstructs organism-specific metabolic pathways and generates a new PGDB that contains the genes, proteins, biochemical reactions and predicted metabolic pathways []. Using the PathoLogic algorithm, the EC numbers, the gene-product names (i.e. protein names) and the G […]

library_books

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

2015
PLoS One
PMCID: 4569324
PMID: 26366735
DOI: 10.1371/journal.pone.0137908

[…] re inferred using Pathway Tools []. Pathways were predicted from the MetaCyc pathway database []. GO terms, EC number and InterPro describers were used as input to generate a Pathway/Genome Database (PGDB) containing the predicted metabolic pathways for each of the given strains.To obtain unbiased information of the metabolic capabilities of the considered Streptococcus strains, we did not use the […]

Citations

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PGDB institution(s)
Department of Urology, Veterans Affairs Medical Center, University of California, San Francisco, CA, USA
PGDB funding source(s)
Supported by National Institutes of Health Grants RO1AG-16870, RO1DK47517, REAP award and VA Merit Review.

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