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KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
In addition to various primary data formats (e.g. GPML, BioPAX, Reactome, [10] KEGG, and RDF [11]), WikiPathways supports a variety of ways to integrate and interact with pathway content. These include directed link-outs, image maps, RSS feeds and deep web services. [12] This enables reuse in projects like COVID19 Disease Map. [13]
To simplify viewing and navigation on the server, and to assist with the topological analyses, all the KEGG pathways in MetPA are presented as a network with metabolites serving as nodes and reactions as edges. MetPA provides an extensive tutorial explaining how to upload data and how interpret its output.
Pathway resources and types of pathway analysis using databases like KEGG, Reactome and WikiPathways. [1]Pathway is the term from molecular biology for a curated schematic representation of a well characterized segment of the molecular physiological machinery, such as a metabolic pathway describing an enzymatic process within a cell or tissue or a signaling pathway model representing a ...
KEGG: Kyoto Encyclopedia of Genes and Genomes Kyoto University Bioinformatics Center: Compounds Glycans (also enzymes, reactions, pathways) CAS ChEBI ChEMBL MASSBANK NIKKAJI PubChem PDB-CCD "KEGG". K i Database: PDSP ligand binding "Ki Database". KNApSAcK Nara Institute of Science and Technology: InChI CAS SMILES organisms C00 "KNApSAcK". LINCS
The ‘KEGG Organisms’ section, which is divided into eukaryotes and prokaryotes, encompasses many organisms for which gene and DNA information can be searched by typing in the enzyme of choice. BioCyc, EcoCyc, and MetaCyc: BioCyc Is a collection of 3,000 pathway/genome databases (as of Oct 2013), with each database dedicated to one organism.
TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. [1] TopHat aligns RNA-Seq reads to mammalian-sized genomes. [2]
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