ArticleSource code for biology and medicine2014
EC2KEGG: a command line tool for comparison of metabolic pathways.
Article in Source code for biology and medicine, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Evolutionary patterns of archaea predominant in acidic environment.Environmental microbiome · 2023Article
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- Genome-scale metabolic model of the rat liver predicts effects of diet restriction.Scientific reports · 2019Article
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- Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae.iScience · 2019Article
- Draft genome sequence of the New Jersey aster yellows strain of 'Candidatus Phytoplasma asteris'.PloS one · 2018Article
- The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations.Database : the journal of biological databases and curation · 2017Article
- Deep Sequencing of Suppression Subtractive Hybridisation Drought and Recovery Libraries of the Non-model CropFrontiers in plant science · 2017Article
- Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations.BMC bioinformatics · 2016Article
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Authors and funding
1 author.
Funding
Abstract
backgroundNext-generation sequencing and metagenome projects yield a large number of new genomes that need further annotations, such as identification of enzymes and metabolic pathways, or analysis of metabolic strategies of newly sequenced species in comparison to known organisms. While methods for enzyme identification are available, development of the command line tools for high-throughput comparative analysis and visualization of identified enzymes is lagging.
methodsA set of perl scripts has been developed to perform automated data retrieval from the KEGG database using its new REST program application interface. Enrichment or depletion in metabolic pathways is evaluated using the two-tailed Fisher exact test followed by Benjamini and Hochberg correction.
resultsComparative analysis of a given set of enzymes with a specified reference organism includes mapping to known metabolic pathways, finding shared and unique enzymes, generating links to visualize maps at KEGG Pathway, computing enrichment of the pathways, listing the non-mapped enzymes.
conclusionsEC2KEGG provides a platform independent toolkit for automated comparison of identified sets of enzymes from newly sequenced organisms against annotated reference genomes. The tool can be used both for manual annotations of individual species and for high-throughput annotations as part of a computational pipeline. The tool is publicly available at http://sourceforge.net/projects/ec2kegg/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.