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HAMAP in 2013, new developments in the protein family classification and annotation system
2012
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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]
2019
bioRxiv
pre-print
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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
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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
2014
Nucleic Acids Research
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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?
2014
Scientometrics
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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
2021
Frontiers in Microbiology
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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
2013
Bioinformatics
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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
2013
Standards in Genomic Sciences
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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
2013
Nucleic Acids Research
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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
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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
2014
Bioinformatics
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2016
Bioinformatics
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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
2020
Frontiers in Genetics
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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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