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PUMA2 specifications


Unique identifier OMICS_04580
Name PUMA2
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for PUMA2

PUMA2 citations


ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities

Adv Bioinformatics
PMCID: 3085309
PMID: 21541071
DOI: 10.1155/2011/743782

[…] nce. There are various databases to aid metabolic reconstruction which integrate and curate data from different sources, for example KEGG [] which combines genomic, chemical, and network information, PUMA2 [] which provides an array of tools for comparative genomics, and MetaCyc [] which is a multiorganism pathway/genome database. Accurate identification of metabolic enzymes from a fully sequenced […]


Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

Genome Biol
PMCID: 2690999
PMID: 19284550
DOI: 10.1186/gb-2009-10-3-r28

[…] , three systems have been described that provide both information on phenotypic properties of genomes and information on their metabolic pathways [-]. However, the Genome Properties system [] and the PUMA2 system [] list all pathways shared by the phenotypically related species rather than extracting only those pathways that are, in fact, associated with the phenotype. Therefore, the list contains […]


The development of PIPA: an integrated and automated pipeline for genome wide protein function annotation

BMC Bioinformatics
PMCID: 2259298
PMID: 18221520
DOI: 10.1186/1471-2105-9-52

[…] integrates these resources is able to predict genome-wide protein function with higher accuracy than any individual method. Large integrated information systems, like InterPro [], BASys [], GenDB [], PUMA2 [], MaGe [], AGMIAL [], and IMG [], are constantly emerging. They include comprehensive resources that allow curators and users alike to gain insights into protein functions. However, these syst […]


The prokaryotic antecedents of the ubiquitin signaling system and the early evolution of ubiquitin like β grasp domains

Genome Biol
PMCID: 1779556
PMID: 16859499
DOI: 10.1186/gb-2006-7-7-r60

[…] families, has been considerably boosted due to the enormous increase in data from the various microbial genome sequencing projects [,] and the development of publicly available resources such as WIT2/PUMA2 and STRING/SMART that integrate a variety of contextual information [-].Accordingly, we set up a protocol to identify comprehensively the network of contextual connections centered on the prokar […]


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PUMA2 institution(s)
Mathematics and Computer Science Division, Argonne National Laboratory Argonne, IL, USA; Computation Institute, University of Chicago Chicago, IL, USA; University of Illinois at Chicago Chicago, IL, USA

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