(Per ordre alfabètic del cognom de l'autor)
The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. Furthermore, BioCyc PGDBs include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.
BioCyc contains 2988 databases as of June 11th (version 17.1). The most comprehensive databases are part of Tier 1 Databases and they are required to have received at least one year of literature-based curation by scientists. Currently they are:
Find below a more detailed description of the most relevant databases for biomedical studies.
ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions.
MetaboHunter is a web server application for semi-automatic assignment of 1D NMR spectra of metabolites. MetaboHunter provides tools for metabolite identification based on spectra or peak lists with three different search methods and with possibility for peak drift in a user defined spectral range. The assignment is performed by comparison with two major publically available databases (HMDB, MMCD) of NMR metabolite standard measurements. In this work we present the Web tool with detailed testing of the methods provided in the Supplementary data.