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Uniclust databases of clustered and deeply annotated protein sequences and alignments

Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger
2016 Nucleic Acids Research  
We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and Uniboost30, as a resource  ...  The Uniclust databases cluster UniProtKB sequences at the level of 90%, 50% and 30% pairwise sequence identity.  ...  ACKNOWLEDGEMENTS We are grateful to Markus Meier (Göttingen) for development of the Uniboost alignment database and to Borisas Bursteinas (EBI) for fruitful discussions.  ... 
doi:10.1093/nar/gkw1081 pmid:27899574 pmcid:PMC5614098 fatcat:6nymu5izqngbrmyq2fgya5p3pi

The Paracaedibacter-like endosymbiont of Bodo saltans (Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association [article]

Samriti Midha, Daniel J Rigden, Stefanos Siozios, Gregory D.D Hurst, Andrew P Jackson
2020 bioRxiv   pre-print
However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems.  ...  Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death.  ...  Uniclust 653 databases of clustered and deeply annotated protein sequences and alignments. A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of 665 large phylogenies.  ... 
doi:10.1101/2020.07.24.217133 fatcat:aywx5b4uzvbjdfrms5uibhpmcy

A Reproducibility Analysis-based Statistical Framework for Residue-Residue Evolutionary Coupling Detection [article]

Yunda Si, Chengfei Yan
2021 bioRxiv   pre-print
from DCA are highly dependent on the number and the length of the homologous sequences forming the multiple sequence alignment, the detailed settings of the DCA algorithm, the functional characteristics  ...  IDR-DCA was applied to select residue pairs for contact prediction for 150 proteins, 30 protein-protein interactions and 36 RNAs, in which we applied three widely used DCA software to perform the DCA.  ...  Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Res. 45, D170-D176 (2017). 27. Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H.  ... 
doi:10.1101/2021.02.01.429092 fatcat:gpgkosewefeevbysldx3td2w6i

Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework

Lewis Moffat, David T Jones
MOTIVATION: Over the past 50 years, our ability to model protein sequences with evolutionary information has progressed in leaps and bounds.  ...  However, even with the latest deep learning methods, the modelling of a critically important class of proteins, single orphan sequences, remains unsolved.  ...  Cuff,J.A. et al. (1998) JPRED: a consensus secondary structure prediction ser- Mirdita,M. et al. (2017) Uniclust databases of clustered and deeply annotated ver.  ... 
doi:10.25418/crick.17142674.v1 fatcat:khjbr5rscjhrdlbqzdx3tibcse

Protein Structure Prediction by Recurrent and Convolutional Deep Neural Network Architectures

Jack Hanson, University, My, Kuldip Paliwal
Protein contact maps describe the intra-sequence distance between each residue pairing at a distance cuto , providing key restraints towards the possible conformations of a protein.  ...  In this thesis, the application of convolutional and recurrent machine learning techniques to several key structural properties of proteins is explored.  ...  Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. Bairoch,A. et al. (2005) The universal protein resource (uniprot).  ... 
doi:10.25904/1912/3830 fatcat:pllucrmcl5cw5nkdvjjpmklgfu