InterProScan 5: genome-scale protein function classification

By Philip Jones, David Binns, Hsin-Yu Chang, M. Fraser, Weizhong Li, C. McAnulla, Hamish McWilliam, John Maslen, Alex L. Mitchell, Gift Nuka and 7 more. Bioinform., 2014

8,123 citations recorded by the source corpus.

Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cab088a022bdce42562ddcae35cd102814f4be4c

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Citations in the corpus

Extensive complementarity between gene function prediction methods (2016, methodology): “Of that, 8.7 bits/gene is assigned directly from experimental data, and the other 15.4 bits/gene is assigned using the commonly-applied electronic annotation methods, per the UniprotGOA database (Camon et al., 2005); many of these annotations derive from InterPro (Jones et al., 2014).”
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants (2016, methodology): “Taking an integrative strategy by combining sequencebased prediction (29), orthologous-based projection, and collection of existing annotation in canonical sources (25,26), we successfully annotated 93.”
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) (2015, methodology): “InterPro Scan: Additional protein family annotations for SMART, PrositeProfiles, PrositePatterns, and SuperFamily are provided by InterPro Scan (run with default parameters) [18].”
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database (2015, methodology): “Using JBrowse, one can view a wide range of informative data tracks including continually updated gene and protein names, regulatory regions, functional domain predictions based on InterProScan 5 (7), genomic island predictions based on IslandViewer 3 (24), curated virulence factor genes and our pat”
InterPro in 2017—beyond protein family and domain annotations (2016, methodology): “Protein annotations derived from InterPro’s member database signatures are calculated using the InterProScan software package (25) on a monthly basis.”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “To enable UniProtKB to perform this annotation task, InterPro matches are calculated on a monthly basis via the Inter-ProScan software package (28), ensuring new sequences are annotated.”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, methodology): “Most tools in use for functional annotation of newly sequenced genomes apply BLAST (Blast2GO, Go¨tz et al. 2008; RAST, Overbeek et al. 2014) or sequence profile-based searches (Finn et al. 2014; Jones et al. 2014) to transfer functional terms from homologous sequences.”
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species (2017, methodology): “Functional information is provided through direct curation, import from the UniProt Knowledgebase (5), or imputation from protein sequence (using the classification tool Inter-ProScan (6)).”
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes (2018, methodology): “1 (15), assignment to a subset of InterPro families using a customized version of InterProScan5 (16) and associating proteins with KEGG Orthology (KO) terms (17) using LAST (18).”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, methodology): “Good examples of such applications are sequence similarity search suites such as NCBI BLAST+ (2), FASTA (3), HMMER3 (4), as well as functional classification and annotation programs such as InterProScan5 (5), which allow large collections of sequence data to be searched.”