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Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

Orla O'Sullivan, John O'Callaghan, Amaia Sangrador-Vegas, Olivia McAuliffe, Lydia Slattery, Pawel Kaleta, Michael Callanan, Gerald F Fitzgerald, R Paul Ross, Tom Beresford
2009 BMC Microbiology  
Comparative genomics of lactic acid bacteria reveals a niche-specific gene set.
doi:10.1186/1471-2180-9-50 pmid:19265535 pmcid:PMC2660350 fatcat:luhk2r2zbnesjmjgeko24axyma

Cloning and characterization of two genes encoding rainbow trout homologues of the IFITM protein family

Mark C. Johnson, Amaia Sangrador-Vegas, Terry J. Smith, Michael T. Cairns
2006 Veterinary Immunology and Immunopathology  
doi:10.1016/j.vetimm.2005.12.007 pmid:16476489 fatcat:ogpk3xntubcb3hqjv65yg5vkiq

The Pfam protein families database: towards a more sustainable future

Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John Tate (+1 others)
2015 Nucleic Acids Research  
In the last two years the Pfam database (http://pfam. xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater
more » ... ty, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automaticallygenerated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.
doi:10.1093/nar/gkv1344 pmid:26673716 pmcid:PMC4702930 fatcat:o7rimhdmlrawdjm6ahqj3yfyhe

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  
Citation details: Sangrador-Vegas,A., Mitchell,A., Chang,H.-Y. et al. GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.  ... 
doi:10.1093/database/baw027 pmid:26994912 pmcid:PMC4799721 fatcat:lwve4cepezbcvi6t2k6odynq4u

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  
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 sites. 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 to classify protein families and domains. InterPro integrates these signatures,
more » ... apitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro Figure 1. InterPro matches for UniProtKB entry Q3JCG5 showing predicted protein family membership, domains and sites.
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

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  
Please refer to any applicable terms of use of the publisher.
doi:10.1093/nar/gkw1107 pmid:27899635 pmcid:PMC5210578 fatcat:wa7z5pgpuffnrh5bf5ycimw7kq

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Alex L Mitchell, Teresa K Attwood, Patricia C Babbitt, Matthias Blum, Peer Bork, Alan Bridge, Shoshana D Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew I Fraser, Julian Gough, David R Haft (+30 others)
2018 Nucleic Acids Research  
The InterPro database (http://www.ebi.ac.uk/ interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic
more » ... nterface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.
doi:10.1093/nar/gky1100 pmid:30398656 fatcat:ccbjkaabarhazk3yclk2vjjqoq

MAJIQ-SPEL: Web-Tool To Interrogate Classical And Complex Splicing Variations From RNA-Seq Data [article]

Christopher Green, Matthew R. Gazzara, Yoseph Barash
2017 bioRxiv   pre-print
Sangrador-Vegas, et al.  ...  background band that does not run true to size. 76 [ 2 ] 762 Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, 77 Marco Punta, Matloob Qureshi, Amaia  ... 
doi:10.1101/136077 fatcat:g6qymezotjfexlth4sg4trgzeq

MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data

Christopher J Green, Matthew R Gazzara, Yoseph Barash, Ivo Hofacker
2017 Bioinformatics  
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, et al.  ... 
doi:10.1093/bioinformatics/btx565 pmid:28968636 fatcat:eam4zgsl4zbrxfrw2ahupxopv4

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
2020 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would like to thank former members of the InterPro team: Sara El-Gebali, Matthew Fraser, Aurélien Luciani, Sebastien Pesseat, Simon Potter, Neil Rawlings, Amaia Sangrador-Vegas  ... 
doi:10.1093/nar/gkaa977 pmid:33156333 pmcid:PMC7778928 fatcat:vfs7k3dxr5bcpbpvxbptj6r46m