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HAMAP in 2013, new developments in the protein family classification and annotation system

I. Pedruzzi, C. Rivoire, A. H. Auchincloss, E. Coudert, G. Keller, E. de Castro, D. Baratin, B. A. Cuche, L. Bougueleret, S. Poux, N. Redaschi, I. Xenarios (+1 others)
2012 Nucleic Acids Research  
Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation  ...  HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap. expasy.org/) is a system for the classification and annotation of protein sequences.  ...  In the context of UniRule, we will continue to maintain the HAMAP protein family profiles as a basis for protein classification and the development of new annotation rules as new functions are discovered  ... 
doi:10.1093/nar/gks1157 pmid:23193261 pmcid:PMC3531088 fatcat:sqtfh5uppnhhdoriuglbtrnlsu

HAMAP in 2015: updates to the protein family classification and annotation system

Ivo Pedruzzi, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Edouard de Castro, Delphine Baratin, Béatrice A. Cuche, Lydie Bougueleret, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios (+1 others)
2014 Nucleic Acids Research  
We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September  ...  Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013.  ...  We also thank Brigitte Boeckmann for critical reading of the manuscript and for help with the phylogenetic analysis of the sirtuin protein family. FUNDING  ... 
doi:10.1093/nar/gku1002 pmid:25348399 pmcid:PMC4383873 fatcat:ft6achqrt5cvdpgiwyrez7b3km

HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes [article]

Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea Auchincloss, Elisabeth COUDERT, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios (+2 others)
2019 bioRxiv   pre-print
protein sequences described in RDF format.  ...  Results: We have translated the rules of our HAMAP proteome annotation pipeline to queries in the W3C standard SPARQL 1.1 syntax and applied them with two off-the-shelf SPARQL engines to UniProtKB/Swiss-Prot  ...  The development of the HAMAP SPARQL rules was also supported by the ELIXIR Implementation study on "A microbial metabolism resource for Systems Biology". Funding for open access charge: SERI.  ... 
doi:10.1101/615294 fatcat:hivb7ymy3zeslmcgmrmnt4opti

UniProt: a hub for protein information

2014 Nucleic Acids Research  
UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year.  ...  We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein.  ...  Both UniRules and SAAS use the hierarchical Inter-Pro classification of protein family and domain signatures (15) as a basis for protein classification and functional annotation.  ... 
doi:10.1093/nar/gku989 pmid:25348405 pmcid:PMC4384041 fatcat:lypqesbtlbcnhofja5ybswdlhq

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  
to classify protein families and domains.  ...  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 In-terPro matches are also used to aid UniProtKB curators in their annotation of Swiss-Prot proteins, and are utilized by the automated systems that add annotation to UniProtKB/TrEMBL.  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

Measuring the scientific impact of e-research infrastructures: a citation based approach?

K. Jonkers, G. E. Derrick, C. Lopez-Illescas, P. Van den Besselaar
2014 Scientometrics  
The bioinformatic e-research infrastructure studied offers common tools used by life scientists to analyse and interpret genetic and protein sequence information.  ...  These e-resources therefore provide an interesting example with which to explore how representative citations are as acknowledgements of knowledge in the life sciences.  ...  Acknowledgments A shorter version of this paper was presented at the ISSI 2013 conference in Vienna (Jonkers et al. 2013 ) and at the IWBBIO 2013 conference in Granada.  ... 
doi:10.1007/s11192-014-1411-7 fatcat:zi3auowwzbgb7nduhdrhelyj7q

Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins

Xiao Fei, Qiuchun Li, John Elmerdahl Olsen, Xinan Jiao
2021 Frontiers in Microbiology  
There is a lack of simple and effective tools to functionally annotate large number of unknown proteins in a personalized and customized workflow.  ...  We anticipate that Duo will be a useful auxiliary tool for personalized and customized protein function research in the future.  ...  HAMAP in 2015: updates to the protein family classification and annotation system.  ... 
doi:10.3389/fmicb.2021.698322 pmid:34475860 pmcid:PMC8406696 fatcat:xwanw3do6zanvhtkmdswju5mku

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

T. Schuepbach, M. Pagni, A. Bridge, L. Bougueleret, I. Xenarios, L. Cerutti
2013 Bioinformatics  
The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation.  ...  One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches.  ...  Funding: This work was funded by a Swiss National Science Foundation (SNSF) project grant (315230-116864) and the Swiss Federal Government through the State Secretariat for Education, Research and Innovation  ... 
doi:10.1093/bioinformatics/btt129 pmid:23505298 pmcid:PMC3634184 fatcat:vvnf3mckifbvhe33jcriytb26a

Complete genome sequence of Ilumatobacter coccineum YM16-304T

Shun Fujinami, Hiromi Takarada, Hiroaki Kasai, Mitsuo Sekine, Seiha Omata, Takeshi Harada, Rieko Fukai, Akira Hosoyama, Hiroshi Horikawa, Yumiko Kato, Hidekazu Nakazawa, Nobuyuki Fujita
2013 Standards in Genomic Sciences  
The functions of predicted protein-coding genes were assigned manually, using the in-house genome annotation system OCSS (unpublished), in comparison with Uniprot [20] , Interpro [21] , HAMAP [22]  ...  is based on the total number of protein coding genes in the annotated genome.  ... 
doi:10.4056/sigs.4007734 pmid:24501628 pmcid:PMC3910706 fatcat:rmb7ann4hze4reqqkoopwy7e7i

Ensembl Genomes 2013: scaling up access to genome-wide data

Paul Julian Kersey, James E. Allen, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall (+21 others)
2013 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would also like to acknowledge the contributions of all our collaborators and of all colleagues working on the Ensembl project.  ...  Bacterial proteins (from all included genomes) have additionally been grouped into families using the HAMAP (28) and Panther (29) resources.  ...  in the system?  ... 
doi:10.1093/nar/gkt979 pmid:24163254 pmcid:PMC3965094 fatcat:bzydx6qowvdunnkte5sioqgk5y

Activities at the Universal Protein Resource (UniProt)

2013 Nucleic Acids Research  
NEW AND ONGOING DEVELOPMENTS UniProt biocuration Manual and automatic annotation in UniProtKB.  ...  The InterPro hierarchy (5) of protein family and domain signatures is used as the basis for protein classification and along with other conditions such as taxonomy and sequence length, triggers application  ... 
doi:10.1093/nar/gkt1140 pmid:24253303 pmcid:PMC3965022 fatcat:ymvqbpyhizafba7upcn222a6ty

InterProScan 5: genome-scale protein function classification

P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn (+5 others)
2014 Bioinformatics  
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  ...  Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan.  ...  ACKNOWLEDGEMENTS The InterPro team would like to acknowledge feedback received from users who tested the various release candidates of InterProScan5 during its development and thank other developers at  ... 
doi:10.1093/bioinformatics/btu031 pmid:24451626 pmcid:PMC3998142 fatcat:kfovtogftvhpbhuwmulywlixha

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong, Robert D. Finn
2016 Database: The Journal of Biological Databases and Curation  
However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used  ...  Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator  ...  For example, InterPro entry IPR030545 represents the WD-repeat-containing protein 62 (WDR62) family. WDR62 is required for cerebral cortical development in vertebrates (18) .  ... 
doi:10.1093/database/baw027 pmid:26994912 pmcid:PMC4799721 fatcat:lwve4cepezbcvi6t2k6odynq4u

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Tunca Doğan, Alistair MacDougall, Rabie Saidi, Diego Poggioli, Alex Bateman, Claire O'Donovan, Maria J. Martin
2016 Bioinformatics  
and propagating functional annotation.  ...  Motivation: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation.  ...  The proposed method also brings new approaches to the field by (i) employing InterPro as the domain annotation source, (ii) the use of multi-label classification technique to annotate proteins with multiple  ... 
doi:10.1093/bioinformatics/btw114 pmid:27153729 pmcid:PMC4965628 fatcat:dwuwcqp4wvclvhyr4fqoqx2gea

Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis

De-Long Guan, Jie Yang, Ying-Kui Liu, Yuan Li, Da Mi, Li-Bin Ma, Zhe-Zhi Wang, Sheng-Quan Xu, Qiang Qiu
2020 Frontiers in Genetics  
Recent studies have focused on artificial culturing, strain optimization, and the identification and development new drugs based on the anticoagulant effects of H. manillensis bites; however, data regarding  ...  Predictions indicated that the assembled genome contained 21,005 protein-coding genes. Up to 17,865 genes were annotated in multiple databases including Gene Ontology.  ...  GO is a standardized gene functional classification system, which comprehensively describes the properties of genes and gene products in organisms.  ... 
doi:10.3389/fgene.2019.01321 pmid:32010187 pmcid:PMC6977106 fatcat:dyl3isucmrf6tffsvmcwacspja
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