Kandlinger, Florian and Plach, Maximilian G. and Merkl, Rainer (2017) AGeNNT: annotation of enzyme families by means of refined neighborhood networks. BMC BIOINFORMATICS, 18: 274. ISSN 1471-2105,
Full text not available from this repository. (Request a copy)Abstract
Background: Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters. The Enzyme Function Initiative (http://enzymefunction.org/) offers services that compute SSNs and GNNs. Results: We have implemented AGeNNT that utilizes these services, albeit with datasets purged with respect to unspecific protein functions and overrepresented species. AGeNNT generates refined GNNs (rGNNs) that consist of cluster-nodes representing the sequences under study and Pfam-nodes representing enzyme functions encoded in the respective neighborhoods. For cluster-nodes, AGeNNT summarizes the phylogenetic relationships of the contributing species and a statistic indicates how unique nodes and GNs are within this rGNN. Pfam-nodes are annotated with additional features like GO terms describing protein function. For edges, the coverage is given, which is the relative number of neighborhoods containing the considered enzyme function (Pfam-node). AGeNNT is available at https://github.com/kandlinf/agennt. Conclusions: An rGNN is easier to interpret than a conventional GNN, which commonly contains proteins without enzymatic function and overly specific neighborhoods due to phylogenetic bias. The implemented filter routines and the statistic allow the user to identify those neighborhoods that are most indicative of a specific metabolic capacity. Thus, AGeNNT facilitates to distinguish and annotate functionally different members of enzyme families.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SEQUENCE SIMILARITY NETWORKS; PROKARYOTIC GENOMES; METABOLIC PATHWAYS; ESCHERICHIA-COLI; WEB TOOL; BIOSYNTHESIS; DATABASE; CLASSIFICATION; VISUALIZATION; SPECIFICITY; Sequence similarity network; SSN; Genome neighborhood network; GNN; Genome content; Enzyme function; Homology-free annotation |
| Subjects: | 500 Science > 530 Physics |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Rainer Merkl |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 14 Dec 2018 13:10 |
| Last Modified: | 20 Feb 2019 14:29 |
| URI: | https://pred.uni-regensburg.de/id/eprint/865 |
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