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SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, Hans-Werner Mewes
2009 Nucleic Acids Research  
The SIMAP database provides a comprehensive and up-to-date precalculation of the protein sequence similarity matrix, sequence-based features and sequence clusters.  ...  Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge the BOINCSIMAP community for donating their CPU power for the calculation of protein similarities and features.  ... 
doi:10.1093/nar/gkp949 pmid:19906725 pmcid:PMC2808863 fatcat:oqjoo4khiffgnoceprxpxjaxk4

SIMAP structuring the network of protein similarities

T. Rattei, P. Tischler, R. Arnold, F. Hamberger, J. Krebs, J. Krumsiek, B. Wachinger, V. Stumpflen, W. Mewes
2007 Nucleic Acids Research  
In order to facilitate the computationally intensive tasks of sequence analysis, the Similarity Matrix of Proteins (SIMAP) database aims to provide a comprehensive and up-to-date dataset of the precalculated  ...  Novel features of SIMAP include a new, portlet-based web portal providing multiple, structured views on retrieved proteins and integration of protein clusters and a unique search method for similar domain  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge the BOINCSIMAP community for donating their CPU power for the calculation of protein similarities and features and especially Jonathan Hoser for his  ... 
doi:10.1093/nar/gkm963 pmid:18037617 pmcid:PMC2238827 fatcat:vt4nmwod2ngynie7nejia53s44

SIMAP: the similarity matrix of proteins

T. Rattei
2006 Nucleic Acids Research  
Similarity Matrix of Proteins (SIMAP) (http://mips.gsf. 10 de/simap) provides a database based on a precomputed similarity matrix covering the similarity space formed by .4 million amino acid sequences  ...  Each sequence in the database is supplemented with pre-calculated features generated by detailed 25 sequence analyses.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this 75 article was provided by the GSF-National Research Center for Environment and Health, Neuherberg.  ... 
doi:10.1093/nar/gkj106 pmid:16381858 pmcid:PMC1347468 fatcat:qtyi2fy46jg3bijfttehhy4vuu

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei
2013 Nucleic Acids Research  
It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional  ...  SIMAP uses the sensitive FASTA search heuristics, the Smith-Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge the BOINCSIMAP community for donating their CPU power for the calculation of protein similarities.  ... 
doi:10.1093/nar/gkt970 pmid:24165881 pmcid:PMC3965014 fatcat:nxbvchfugjd6pa7u7whwbn7idq

Gene3D: comprehensive structural and functional annotation of genomes

C. Yeats, J. Lees, A. Reid, P. Kellam, N. Martin, X. Liu, C. Orengo
2007 Nucleic Acids Research  
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources.  ...  CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships  ...  similarity data and hosting the CATH HMMs on the SIMAP BOINC system.  ... 
doi:10.1093/nar/gkm1019 pmid:18032434 pmcid:PMC2238970 fatcat:lghlvfauxfahhhyem5g5ltqqfa

MIPS: analysis and annotation of genome information in 2007

H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Munsterkotter, A. Ruepp, M. Spannagl, V. Stumpflen, T. Rattei
2007 Nucleic Acids Research  
of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an  ...  CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification  ...  We thank Biomax Informatics AG for providing the PEDANT Genome Annotation System.  ... 
doi:10.1093/nar/gkm980 pmid:18158298 pmcid:PMC2238900 fatcat:3xeojdnfnngg7nd3lelf6tieke

MIPS: curated databases and comprehensive secondary data resources in 2010

H. Werner Mewes, Andreas Ruepp, Fabian Theis, Thomas Rattei, Mathias Walter, Dmitrij Frishman, Karsten Suhre, Manuel Spannagl, Klaus F.X. Mayer, Volker Stümpflen, Alexey Antonov
2010 Nucleic Acids Research  
The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences.  ...  The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological  ...  Similarity Matrix of Proteins: exhaustive protein similarity matrix The Similarity Matrix of Proteins (SIMAP) is an exhaustive, up-to-date database of pre-calculated similarities and features of protein  ... 
doi:10.1093/nar/gkq1157 pmid:21109531 pmcid:PMC3013725 fatcat:ovrbatthcnb7vbb7bgntbu2mha

Effective--a database of predicted secreted bacterial proteins

M.-A. Jehl, R. Arnold, T. Rattei
2010 Nucleic Acids Research  
protein domains and the recognition of signal peptides in amino acid sequences.  ...  Effective (http://effectors.org) is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identification of eukaryotic-like  ...  ACKNOWLEDGEMENTS We thank Tanja Bieber and Dominik Lindner for their help in implementing and setting up the Effective web portal.  ... 
doi:10.1093/nar/gkq1154 pmid:21071416 pmcid:PMC3013723 fatcat:blhl2uqjbjgfpi5pu37v55nuhy

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork
2018 Nucleic Acids Research  
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations.  ...  Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets.  ...  Compared to similar databases, eggNOG focuses on providing: (i) comprehensive functional annotations for the inferred orthologs, (ii) predictions across thousands of genomes covering the three domains  ... 
doi:10.1093/nar/gky1085 pmid:30418610 fatcat:7gq2yqm3hjgspetm2c36xd3c3u

PairsDB atlas of protein sequence space

Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm
2007 Nucleic Acids Research  
Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy.  ...  Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them.  ...  ACKNOWLEDGEMENTS PairsDB integrates data from a variety of sources and we would like to thank the members of the UniProt, ENSEMBL, RefSeq, PDB teams for their efforts and their generous release of data  ... 
doi:10.1093/nar/gkm879 pmid:17986464 pmcid:PMC2238971 fatcat:prehbzvsmjahpdc6t2xkhv5yqi

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences

C. Yeats, J. Lees, P. Carter, I. Sillitoe, C. Orengo
2011 Nucleic Acids Research  
We have constructed a set of web services that provide programmatic access to this integrated database, as well as the Gene3D domain recognition tool (Gene3DScan) and protein sequence annotation pipeline  ...  The Gene3D structural domain database provides domain annotations for 7 million proteins, based on the manually curated structural domain superfamilies in CATH.  ...  ACKNOWLEDGEMENTS We would like to thank Pfam for providing their domain drawing JavaScript library to us.  ... 
doi:10.1093/nar/gkr438 pmid:21646335 pmcid:PMC3125800 fatcat:z4ad5t3odjelnehmlous4cucpe

The Basics of Protein Sequence Analysis [chapter]

Katarzyna H. Kaminska, Kaja Milanowska, Janusz M. Bujnicki
2008 Prediction of Protein Structures, Functions, and Interactions  
KHK has worked on this article while being supported by a fellowship from EMBO and a travel grant from Polish Academy of Sciences and JSPS.  ...  Acknowledgements We thank present and former members of the Bujnicki lab in IIMCB and at the UAM for stimulating discussions and contribution of ideas and information to this article.  ...  A and one protein with domains A and B may be chained to a cluster composed of proteins with domain B and one protein with domains B and C, then chained to a cluster of domains C and so on).  ... 
doi:10.1002/9780470741894.ch1 fatcat:5mafpeqhyjadlme2dmsl7weymq

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering (+1 others)
2015 Nucleic Acids Research  
eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations.  ...  The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group.  ...  ACKNOWLEDGEMENTS Valuable feedback helping to guide some of the improvements to eggNOG was received within the Quest for Orthologs initiative.  ... 
doi:10.1093/nar/gkv1248 pmid:26582926 pmcid:PMC4702882 fatcat:cdzsgymezrd7hbk373no5tmpxy

Metabolic reprogramming by viruses in the sunlit and dark ocean

Bonnie L Hurwitz, Steven J Hallam, Matthew B Sullivan
2013 Genome Biology  
Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.  ...  Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks.  ...  SIMAP is a comprehensive and consolidated protein data set derived from Genbank, PDB, RefSeq, SwissProt, and Trembl, which provides pre-computed protein domains and annotation, thereby facilitating computation  ... 
doi:10.1186/gb-2013-14-11-r123 pmid:24200126 pmcid:PMC4053976 fatcat:ww7j64rkc5gk3etnfi2snjc5fy

Assessment of the developmental success of Anopheles coluzzii larvae under different nutrient regimes: effects of diet quality, food amount and larval density

Patric Stephane Epopa, Hamidou Maiga, Domonbabele François de Sales Hien, Roch Kounbobr Dabire, Rosemary Susan Lees, Jeremie Giles, Frederic Tripet, Thierry Baldet, David Damiens, Abdoulaye Diabate
2018 Malaria Journal  
Jane Morris for discussions and in-depth reading of this manuscript. We thank Dr. Henri Vial for fruitful discussions, and Dr. Clotilde Claudel-Renard and Dr.  ...  EGEE-II is a project funded by the European Union under contract number INFSO-RI-031688. This publication was further supported by the New Partnership for Africa's Development (NEPAD), African Union.  ...  1,424 1,310 1,340 % of coding genome 53 66 29 9 Initial annotation based on sequence similarity (BLAST or *Smith-Waterman E-values) Proportion of predicted protein sequences: -having a detectable  ... 
doi:10.1186/s12936-018-2530-z fatcat:nlobxtvlljhyxpb2rz4iml4hjy
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