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Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

S. Burge, E. Kelly, D. Lonsdale, P. Mutowo-Muellenet, C. McAnulla, A. Mitchell, A. Sangrador-Vegas, S.-Y. Yong, N. Mulder, S. Hunter
2012 Database: The Journal of Biological Databases and Curation  
To aid with interpretation of results, InterPro entries are manually annotated with terms from the Gene Ontology (GO).  ...  InterPro amalgamates predictive protein signatures from a number of well-known partner databases into a single resource.  ...  Acknowledgements We thank Emily Dimmer and Claire O'Donovan for their critical reading of this manuscript and Tony Sawford for assistance with protein match counts. Conflict of interest.  ... 
doi:10.1093/database/bar068 pmid:22301074 pmcid:PMC3270475 fatcat:mczeyk6qqrhxpn2aysoyqgocde

EnzML: multi-label prediction of enzyme classes using InterPro signatures

Luna De Ferrari, Stuart Aitken, Jano van Hemert, Igor Goryanin
2012 BMC Bioinformatics  
In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function.  ...  EnzML was evaluated using a standard set of 300,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commission (EC) annotations.  ...  JVH and IG helped conceive the study, participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.  ... 
doi:10.1186/1471-2105-13-61 pmid:22533924 pmcid:PMC3483700 fatcat:vzg3akvnrbbwxa7uwps6khslnm

Enzyme mechanism prediction: a template matching problem on InterPro signature subspaces

Hamse Y. Mussa, Luna De Ferrari, John B. O. Mitchell
2015 BMC Research Notes  
Our results also dovetail well with another finding we reported, namely that InterPro signatures are critical for accurate prediction of enzyme mechanism.  ...  We recently reported that one may be able to predict with high accuracy the chemical mechanism of an enzyme by employing a simple pattern recognition approach: a k Nearest Neighbour rule with k = 1 (k  ...  Acknowledgements We thank the BBSRC for funding this research through grant BB/I00596X/1 and are also grateful to the Scottish Universities Life Sciences Alliance (SULSA) for financial support.  ... 
doi:10.1186/s13104-015-1730-7 pmid:26634450 pmcid:PMC4669639 fatcat:ojaebs6fbvgefat4eal2tdziiq

The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches  ...  The InterPro database (http://www.ebi.ac.uk/ interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and  ...  The considerable power of InterPro in propagating annotation is illustrated in the targeted GO curation work.  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

M. C. Costanzo, J. Park, R. Balakrishnan, J. M. Cherry, E. L. Hong
2011 Database: The Journal of Biological Databases and Curation  
Using this method, we show that comparison of manually assigned 'unknown' annotations in the Saccharomyces Genome Database (SGD) with InterPro-based predictions can identify annotations that need to be  ...  Because literature-based GO annotations are often used to propagate functional predictions between related proteins, their accuracy is critically important.  ...  Reddy, Ralf Stephan, and Kimberly van Auken for assistance in determining counts of genes and annotations in other databases; and all members of the SGD project for helpful discussions and support.  ... 
doi:10.1093/database/bar004 pmid:21411447 pmcid:PMC3067894 fatcat:jaxwcnpsffhahj5n2p7q37g5ka

Applications of InterPro in protein annotation and genome analysis

M. Biswas
2002 Briefings in Bioinformatics  
Manually merging entries for proteins predicted by genome submission with pre-existing entries is a priority task for the curators of SWISS-PROT.  ...  The assignment of GO terms to InterPro entries was done by manual inspection of the abstract of the entries and annotation of proteins in the match lists, and mapping of the appropriate GO terms of any  ... 
doi:10.1093/bib/3.3.285 pmid:12230037 fatcat:3p33ikuxqbdenlf6yd6tok3aaa

InterPro in 2017—beyond protein family and domain annotations

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
2016 Nucleic Acids Research  
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites.  ...  Here, we report recent developments with InterPro and its associated software, in-cluding the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and  ...  CDD is a manually curated protein annotation resource representing domain footprints conserved in molecular evolution.  ... 
doi:10.1093/nar/gkw1107 pmid:27899635 pmcid:PMC5210578 fatcat:wa7z5pgpuffnrh5bf5ycimw7kq

Functional annotation of parasitic worm genomes, by assigning protein names and GO terms

Avril Coghlan, Avril Coghlan, Matthew Berriman
2018 Protocol Exchange  
Given a set of predicted protein-coding genes for a newly sequenced genome, functional annotation involves assigning putative functions to the predicted genes.  ...  Two ways in which this can be done are assigning protein names and Gene Ontology (GO) terms to the predicted proteins.  ...  Figures 10 Figure 1 Example of protein naming  ... 
doi:10.1038/protex.2018.055 fatcat:yll22lcxbrhyjcgis62eew7iqy

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+45 others)
2012 Nucleic Acids Research  
Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function.  ...  InterPro has utility in the large-scale analysis of whole genomes and metagenomes, as well as in characterizing individual protein sequences.  ...  InterPro entries are manually annotated with these terms, allowing GO terms to be inferred for sequences that match the entries.  ... 
doi:10.1093/nar/gks456 pmcid:PMC3378909 fatcat:oqmafftblfcmdgh4a3i4nzqpzu

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+38 others)
2011 Nucleic Acids Research  
InterPro entries are manually annotated with these terms, allowing GO terms to be inferred for sequences that match the entries.  ...  These data are also used to aid UniProtKB curators in their annotation of Swiss-Prot proteins and are utilized by the automatic system that adds annotation to UniProtKB/TrEMBL.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr948 pmid:22096229 pmcid:PMC3245097 fatcat:awtdl7qobjhnveofe7jxno6ju4

Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein

Masayuki Tanaka, Takashi Makiuchi, Tomoyoshi Komiyama, Takashi Shiina, Ken Osaki, Hiroshi Tachibana, Ananias A. Escalante
2019 PLoS Neglected Tropical Diseases  
To explore the molecular signatures of host-parasite interactions, we conducted de novo assembly of the E. nuttalli genome, utilizing self-correction of PacBio long reads and polishing corrected reads  ...  GO-term enrichment analysis of mammalian host-related molecules indicated diversification of transmembrane proteins, including AIG1 family and BspA-like proteins that may be involved in the host-parasite  ...  Kazuyoshi Hosomichi of the National Institute of Genetics for Entamoeba nuttalli genome and host specificity of Entamoeba spp.  ... 
doi:10.1371/journal.pntd.0007923 pmid:31805050 pmcid:PMC6917348 fatcat:4uzpshg6prhc5bzjp33rv3lwxa

Bioinformatics Tools for the Next Generation of Metal Biotechnology [chapter]

Hideki Nakayama
2011 Handbook of Metal Biotechnology  
The family database currently comprises more than 1600 manually curated orthologous protein families that belong to one of the HAMAP families.  ...  The SMART (release 6.0) contains manually curated models for 784 protein domains. The underlying protein database is based on completely sequenced genomes of 630 species.  ... 
doi:10.1201/b11762-18 fatcat:ah2bxdxbrbfgfcmhfgi53nw4re

Using FlyBase to Find Functionally Related Drosophila Genes [chapter]

Alix J. Rey, Helen Attrill, Steven J. Marygold
2018 Msphere  
This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their  ...  These are compiled manually from the published literature or expert databases and greatly facilitate access to, and analysis of, established gene sets.  ...  GO annotations may be added manually by a curator based either on experimental data in published research (e.g., direct assay, genetic interaction) or from predictions/assertions based on sequence, such  ... 
doi:10.1007/978-1-4939-7737-6_16 pmid:29761468 pmcid:PMC5996772 fatcat:4s77pj47u5gbfmo57eaa6jefl4

The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro

E. Camon
2003 Genome Research  
These authors contributed equally to this work. 4 Corresponding author. E-MAIL camon@ebi.ac.uk; FAX +44 0 1223 494 468. Article and publication are at  ...  The associated GO term therefore applies to all proteins with true hits to all signatures in the InterPro entry.  ...  On the other hand, electronic techniques offer a much quicker approach to the assignment of GO terms to new data while enabling a retrofit of GO annotation to previously curated data.  ... 
doi:10.1101/gr.461403 pmid:12654719 pmcid:PMC430163 fatcat:y33clngkn5g2pb7eegoclhgbvq

Towards region-specific propagation of protein functions [article]

Da Chen Emily Koo, Richard Bonneau
2018 bioRxiv   pre-print
Due to the nature of experimental annotation, most protein function prediction methods operate at the protein-level, where functions are assigned to full-length proteins based on overall similarities.  ...  protein-level temporal holdout predictive performances to expand the variety and specificity of GO terms we could evaluate.  ...  Currently, a few such annotated domaincentric resources exist through a combination of manual and automated curation (e.g.  ... 
doi:10.1101/275487 fatcat:uteeq6xaqvgkrfoq5yzdox3l3e
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