dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
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Cantarel, 2009, The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Res., 37, D233
Ekstrom, 2014, PlantCAZyme: a database for plant carbohydrate-active enzymes, Database, 2014, bau079
Huang, 2018, dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation, Nucleic Acids Res., 46, D516
Yin, 2012, dbCAN: a web resource for automated carbohydrate-active enzyme annotation, Nucleic Acids Res., 40, W445
Cockburn, 2016, Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease, J. Mol. Biol., 428, 3230
Flint, 2012, Microbial degradation of complex carbohydrates in the gut, Gut Microbes, 3, 289
El Kaoutari, 2013, The abundance and variety of carbohydrate-active enzymes in the human gut microbiota, Nat. Rev. Microbiol., 11, 497
Rogowski, 2015, Glycan complexity dictates microbial resource allocation in the large intestine, Nat. Commun., 6, 7481
Krumbeck, 2016, Prebiotics and synbiotics: dietary strategies for improving gut health, Curr. Opin. Gastroenterol., 32, 110
Lombard, 2014, The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res., 42, D490
Terrapon, 2017, A Practical Guide to Using Glycomics Databases, 117
Finn, 2011, HMMER web server: interactive sequence similarity searching, Nucleic Acids Res., 39, W29
Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389
Park, 2010, CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database, Glycobiology, 20, 1574
Busk, 2017, Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function, BMC Bioinformatics, 18, 214
Busk, 2013, Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs, Appl. Environ. Microbiol., 79, 3380
Kultima, 2016, MOCAT2: a metagenomic assembly, annotation and profiling framework, Bioinformatics (Oxford, England), 32, 2520
Kuan, 2016, DemaDb: an integrated dematiaceous fungal genomes database, Database, 2016, baw008
Mende, 2017, proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes, Nucleic Acids Res., 45, D529
Jones, 2018, SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets, Biotechnol. Biofuels, 11, 27
Hyatt, 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119
Rho, 2010, FragGeneScan: predicting genes in short and error-prone reads, Nucleic Acids Res., 38, e191
Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59
Bjursell, 2006, Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period, J. Biol. Chem., 281, 36269
Terrapon, 2018, PULDB: the expanded database of Polysaccharide Utilization Loci, Nucleic Acids Res., 46, D677
Grondin, 2017, Polysaccharide utilization loci: fueling microbial communities, J.Bacteriol., 199, e00860-16
Petersen, 2011, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat. Methods, 8, 785
