, , 1997.
, Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research, vol.25, pp.3389-3402
Continuous distributed representation of biological sequences for deep proteomics and genomics, PloS one, vol.10, issue.11, p.141287, 2015. ,
Properties and identification of human protein drug targets, Bioinformatics, vol.25, issue.4, pp.451-457, 2009. ,
Computational biology in the 21st century: Scaling with compressive algorithms, Commun. ACM, vol.59, issue.8, pp.72-80, 2016. ,
Enzyme family classification by support vector machines, Proteins: Structure, Function, and Bioinformatics, vol.55, issue.1, pp.66-76, 2004. ,
Svm-prot: web-based support vector machine software for functional classification of a protein from its primary sequence, Nucleic acids research, vol.31, issue.13, pp.3692-3697, 2003. ,
Predicting enzyme subclass by functional domain composition and pseudo amino acid composition, Journal of Proteome Research, vol.4, issue.3, pp.967-971, 2005. ,
Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology, Current Proteomics, vol.6, issue.4, pp.262-274, 2009. ,
Current IUBMB recommendations on enzyme nomenclature and kinetics. Perspectives in Science, vol.1, pp.74-87, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01494614
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature, BMC Bioinformatics, vol.19, issue.1, p.334, 2018. ,
Prediction of enzyme classification from protein sequence without the use of sequence similarity, Proc Int Conf Intell Syst Mol Biol, vol.5, pp.92-99, 1997. ,
Predicting enzyme class from protein structure without alignments, Journal of molecular biology, vol.345, issue.1, pp.187-199, 2005. ,
HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.2, pp.29-37, 2011. ,
Cdhit: accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, issue.23, pp.3150-3152, 2012. ,
Automated annotation of microbial proteomes in SWISS-PROT, Computational Biology and Chemistry, vol.27, issue.1, pp.49-58, 2003. ,
Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method, Biosystems, vol.90, issue.2, pp.405-413, 2007. ,
Interproscan 5: genomescale protein function classification, Bioinformatics, vol.30, issue.9, pp.1236-1240, 2014. ,
, Fasttext.zip: Compressing text classification models, 2016.
Bag of tricks for efficient text classification, Proceedings of the 15th Conference of the European Chapter, vol.2, pp.427-431, 2017. ,
, Distributed representations for biological sequence analysis, 2016.
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT, Bioinformatics, vol.17, pp.920-926, 2001. ,
Eficaz2. 5: application of a high-precision enzyme function predictor to 396 proteomes, Bioinformatics, vol.28, issue.20, pp.2687-2688, 2012. ,
Protein domain organisation: adding order, BMC Bioinformatics, vol.10, issue.1, p.39, 2009. ,
DEEPre: sequence-based enzyme EC number prediction by deep learning, Bioinformatics, vol.34, issue.5, pp.760-769, 2018. ,
Svm-prot 2016: a web-server for machine learning prediction of protein functional families from sequence irrespective of similarity, PloS one, vol.11, issue.8, p.155290, 2016. ,
ECS: an automatic enzyme classifier based on functional domain composition, Computational Biology and Chemistry, vol.31, issue.3, pp.226-232, 2007. ,
A novel representation of protein sequences for prediction of subcellular location using support vector machines, Protein Science, vol.14, issue.11, pp.2804-2813, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00433582
Distributed representations of words and phrases and their compositionality, Advances in neural information processing systems, pp.3111-3119, 2013. ,
Interpro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic acids research, vol.47, pp.351-360, 2018. ,
Prediction of detailed enzyme functions and identification of specificity determining residues by random forests, PLoS One, issue.1, p.9, 2014. ,
Efficiency analysis of KNN and minimum distance-based classifiers in enzyme family prediction, Computational Biology and Chemistry, vol.33, issue.6, pp.461-464, 2009. ,
EnzymeDetector: an integrated enzyme function prediction tool and database, BMC Bioinformatics, vol.12, issue.1, p.376, 2011. ,
InterProScan: protein domains identifier, Nucleic Acids Research, vol.33, issue.2, pp.116-120, 2005. ,
EC-BLAST: a tool to automatically search and compare enzyme reactions, Nature Methods, vol.11, issue.2, p.171, 2014. ,
Ezypred: a top-down approach for predicting enzyme functional classes and subclasses, Biochemical and biophysical research communications, vol.364, issue.1, pp.53-59, 2007. ,
, UniProt: a hub for protein information, The UniProt Consortium, vol.43, pp.204-212, 2015.
The i-tasser suite: protein structure and function prediction, Nature methods, vol.12, issue.1, p.7, 2015. ,
, , 2009.
, Genome-wide enzyme annotation with precision control: Catalytic families (CatFam) databases, Proteins: Structure, Function, and Bioinformatics, vol.74, issue.2, pp.449-460