PRIAM statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PRIAM specifications

Information


Unique identifier OMICS_15060
Name PRIAM
Alternative name PRofils pour l’Identification Automatisée du Métabolisme
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Daniel Kahn

Information


Unique identifier OMICS_15060
Name PRIAM
Alternative name PRofils pour l’Identification Automatisée du Métabolisme
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
NCBI BLAST
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Daniel Kahn

Publication for PRofils pour l’Identification Automatisée du Métabolisme

PRIAM citations

 (77)
library_books

A benzene degrading nitrate reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

2018
Sci Rep
PMCID: 5852087
PMID: 29540736
DOI: 10.1038/s41598-018-22617-x

[…] lculated with subread version 1.4.6.The proteins were annotated with KAAS, with SBH and ghostX as settings and with InterProScan 5.6-48.0. The annotation was further enhanced by adding EC numbers via PRIAM version March 06, 2013. Further EC numbers were derived by text mining and matching all InterproScan derived domain names against the BRENDA database (download 13.06.13). This text mining was do […]

library_books

Network Analyses in Plant Pathogens

2018
Front Microbiol
PMCID: 5797656
PMID: 29441045
DOI: 10.3389/fmicb.2018.00035

[…] matic Annotation Server (KAAS) (Moriya et al., ), Reconstruction, Analysis, and Visualization of Metabolic Networks (RAVEN) (Agren et al., ), PRofils pour l'Identification Automatique du Métabolisme (PRIAM) (Claudel-Renard et al., ), SuBliMinal, and Pathway Tools (Swainston et al., ). Furthermore, protocols for supervised and manual reconstruction of metabolic networks have been established (Franc […]

call_split

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca

2018
Sci Rep
PMCID: 5772498
PMID: 29343788
DOI: 10.1038/s41598-017-18378-8
call_split See protocol

[…] protothecoides, Helicosporidium sp., P. cutis, and P. stagnora were classified into known gene families using TreeFam 9 with an E-value cut-off of 1E-5. Plastid-related proteins were identified using PRIAM (March 2015) with an E-value cut-off of 1E-10. […]

library_books

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

2018
Genome Biol Evol
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] () was used to classify the genes and to predict domains and sites. At runtime, the following databases were selected: TIGRFAM, ProDom, SMART, PROSITE, PfamA, PRINTS, SUPERFAMILY, Coils, and Gene3d. PRIAM (), SignalP 4.0 (), and TMHMM () were used to assign Enzyme Commission numbers (ECs), to detect signal peptides, and to detect transmembrane protein topology, respectively. Predictions and prove […]

library_books

Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions

2017
Front Plant Sci
PMCID: 5715477
PMID: 29250098
DOI: 10.3389/fpls.2017.02060

[…] The GSM of O.s. indica was reconstructed starting with its protein sequences available in the NCBI protein database. The protein sequences were subjected to PRIAM (). PRIAM allows automated enzyme detection by mapping the query sequence against PRIAM profiles. It has been used on several bacterial species (; ; ) and also, on oilseed species Ricinus commun […]

call_split

Aspergillus niger Secretes Citrate to Increase Iron Bioavailability

2017
Front Microbiol
PMCID: 5539119
PMID: 28824560
DOI: 10.3389/fmicb.2017.01424
call_split See protocol

[…] The protein products of the expressed genes were annotated using PRIAM (Claudel-Renard et al., ), and subsequently assigned to KEGG pathway maps (Kanehisa and Goto, ; Kanehisa et al., ). Metabolic pathway enrichment analysis was performed using the hypergeometric t […]

Citations

Looking to check out a full list of citations?

PRIAM institution(s)
Laboratoire de Génétique Cellulaire, INRA, Toulouse, France; Laboratoire des Interactions Plantes Micro-organismes, INRA/CNRS, Castanet-Tolosan, France
PRIAM funding source(s)
This work was supported in part by the French Ministry of Education and by the Toulouse-Midi Pyrénées Genopole.

PRIAM reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PRIAM