Efficient system wide metabolic pathway comparisons in multiple microbes using genome to KEGG orthology (G2KO) pipeline tool
Abstract Comparison of system-wide metabolic pathways among microbes provides
valuable insights of organisms' metabolic capabilities that can further assist in rationally …
valuable insights of organisms' metabolic capabilities that can further assist in rationally …
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database
Background Concurrent with the efforts currently underway in mapping microbial genomes
using high-throughput sequencing methods, systems biologists are building metabolic …
using high-throughput sequencing methods, systems biologists are building metabolic …
[PDF][PDF] CARMEN-Comparative analysis and in silico reconstruction of organism-specific metabolic networks
J Schneider, FJ Vorhölter, E Trost, J Blom, YR Musa… - Genet Mol …, 2010 - academia.edu
New sequencing technologies provide ultra-fast access to novel microbial genome data. For
their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction …
their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction …
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
Background Constraint-based modeling is a widely used and powerful methodology to
assess the metabolic phenotypes and capabilities of an organism. The starting point and …
assess the metabolic phenotypes and capabilities of an organism. The starting point and …
[HTML][HTML] KEMET–A python tool for KEGG Module evaluation and microbial genome annotation expansion
Background The rapid accumulation of sequencing data from metagenomic studies is
enabling the generation of huge collections of microbial genomes, with new challenges for …
enabling the generation of huge collections of microbial genomes, with new challenges for …
[HTML][HTML] Pathway tools management of pathway/genome data for microbial communities
The Pathway Tools (PTools) software provides a suite of capabilities for storing and
analyzing integrated collections of genomic and metabolic information in the form of …
analyzing integrated collections of genomic and metabolic information in the form of …
MPA_Pathway_Tool: user-friendly, automatic assignment of microbial community data on metabolic pathways
D Walke, K Schallert, P Ramesh, D Benndorf… - International journal of …, 2021 - mdpi.com
Taxonomic and functional characterization of microbial communities from diverse
environments such as the human gut or biogas plants by multi-omics methods plays an ever …
environments such as the human gut or biogas plants by multi-omics methods plays an ever …
Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict
The reconstruction of complete microbial metabolic pathways using 'omics data from
environmental samples remains challenging. Computational pipelines for pathway …
environmental samples remains challenging. Computational pipelines for pathway …
Genome-scale reconstructions to assess metabolic phylogeny and organism clustering
Approaches for systematizing information of relatedness between organisms is important in
biology. Phylogenetic analyses based on sets of highly conserved genes are currently the …
biology. Phylogenetic analyses based on sets of highly conserved genes are currently the …
MetaPathPredict: A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes
The reconstruction of complete microbial metabolic pathways using 'omics data from
environmental samples remains challenging. Computational pipelines for pathway …
environmental samples remains challenging. Computational pipelines for pathway …