Protein function prediction software tools | Sequence data analysis

Provides functional analysis of protein sequences. InterPro is a software which allows to classify sequences into protein families and to predict the presence of important domains and sites. The software combines predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains.

Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.

Allows automated protein structure prediction and structure-based function annotation. I-TASSER constructs, starting from the amino acid sequence, 3D structural models by reassembling fragments excised from threading templates. I-TASSER servers provides a confidence score (C-score) to estimate the models’ global accuracy. The I-TASSER Suite pipeline was tested in community-wide structure and function prediction experiments, including CASP10 and CAMEO.

Predicts the possible impact of an amino acid substitution on the structure and function of a human protein. PolyPhen predicts the functional significance of an allele replacement from its individual features by a Naïve Bayes classifier. The web application allows users to (i) predict the effect of a single-residue substitution or reference single nucleotide polymorphism SNP, (ii) analyze SNPs in a batch mode, and (iii) search in a database of precomputed predictions for the whole human exome sequence space.

Provides a suite of methods important for the prediction of protein structural and functional features. predictProtein is a web server that incorporates over 30 tools. This software searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. It can help when little is known about the protein in question. For medium-to-high throughput analyses, downloadable software packages and the PredictProtein Machine Image (PPMI) are available.

Detects homology. FFAS includes adding optimized structural features (experimental or predicted), ‘symmetrical’ Z-score calculation and re-ranking the templates with a neural network. It has high success rate at the Structural Classification of Proteins (SCOP) family, superfamily and fold levels. The tool was tested on the Lindahl benchmark set for fold recognition and showed superior success rate on the family and superfamily levels.

Allows to predict protein function. The Argot strategy treats the grouping of Gene Ontology (GO) terms by means of semantic similarity in order to infer protein function. Compared to the previous version, the 2.5 version allows users to realize the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits. It’s also possible with the application of taxonomic constraints to classify annotations that cannot be applied to proteins belonging to the species through investigation.