CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms
| Autor: | Jiankang Tan, Drew Hockaday, Gaoyang Li, Nicholas Ho, Huansheng Cao, Wei Du, Landon Jenkins |
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| Rok vydání: | 2020 |
| Předmět: |
Cyanobacteria
0303 health sciences biology 030306 microbiology Repertoire Harmful Algal Bloom Knowledge Bases Genome scale Computational biology biology.organism_classification Stress resistance Genome Algal bloom 03 medical and health sciences Databases Genetic Biochemical reactions KEGG Molecular Biology Genome Bacterial 030304 developmental biology Information Systems |
| Zdroj: | Briefings in bioinformatics. 22(4) |
| ISSN: | 1477-4054 |
| Popis: | CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH. |
| Databáze: | OpenAIRE |
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