Unknown

Dataset Information

0

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

ABSTRACT: Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, a web server developed to predict protein function from a combination of three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein interaction network data to derive consensus predictions for GO terms using functional enrichment. The INGA server can be queried both programmatically through RESTful services and through a web interface designed for usability. The latter provides output supporting the GO term predictions with the annotating sequences. INGA is validated on the CAFA-1 data set and was recently shown to perform consistently well in the CAFA-2 blind test. The INGA web server is available from URL: http://protein.bio.unipd.it/inga.

SUBMITTER: Piovesan D 

PROVIDER: S-EPMC4489281 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

Piovesan Damiano D   Giollo Manuel M   Leonardi Emanuela E   Ferrari Carlo C   Tosatto Silvio C E SC  

Nucleic acids research 20150527 W1

Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, a web server developed to predict protein function from a combination of three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein interaction network data to derive consensus predictions for G  ...[more]

Similar Datasets

Unknown Effusion: prediction of protein function from sequence similarity networks.
| S-EPMC6361244 | biostudies-literature
Unknown Prediction of enzyme function by combining sequence similarity and protein interactions.
| S-EPMC2430716 | biostudies-literature
Unknown Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks.
| S-EPMC3584933 | biostudies-literature
Unknown Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.
| S-EPMC4965129 | biostudies-literature
Unknown Wei2GO: weighted sequence similarity-based protein function prediction.
| S-EPMC8855713 | biostudies-literature
Unknown COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information.
| S-EPMC5793808 | biostudies-literature
Unknown INGA 2.0: improving protein function prediction for the dark proteome.
| S-EPMC6602455 | biostudies-literature
Unknown Function prediction from networks of local evolutionary similarity in protein structure.
| S-EPMC3584919 | biostudies-literature
Unknown EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches.
| S-EPMC515322 | biostudies-literature
Unknown QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs.
| S-EPMC9403031 | biostudies-literature