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PANTHER / Protein ANalysis THrough Evolutionary Relationships
A widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life. Phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events. Functional annotations are regularly updated using the models generated by the Gene Ontology Phylogenetic Annotation Project.
UniProt-DAAC / UniProt Domain Architecture Alignment and Classification
A method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of UniProt-DAAC was measured through a cross-validation analysis using the Gene Ontology annotation of a sub-set of Uni-ProtKB/Swiss-Prot. The results indicate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85.
SPiCE / Sequence-based Protein Classification and Exploration
Classifies and allows investigations of sequence-based protein. SPiCE gives users functions to manage feature extraction, protein sequence data and the labeled feature matrix. It permits to visualize the resulting feature matrix, and to train and test classifiers for predicting class labels, enabling quick exploration of sets of labeled proteins. This tool offers a way to perform customized and/or computationally expensive tasks on a local computer.
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