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Publication for PUMA2
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities
[…] 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
[…] , 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
[…] 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
[…] 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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