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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  
High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein  ...  More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research.  ...  gold standards, integrating factual information and the biological knowledge as extracted from the literature; (ii) large-scale and comprehensive databases of secondary data such as (1) SIMAP, the exhaustive  ... 
doi:10.1093/nar/gkq1157 pmid:21109531 pmcid:PMC3013725 fatcat:ovrbatthcnb7vbb7bgntbu2mha

iRootHair: A Comprehensive Root Hair Genomics Database

M. Kwasniewski, U. Nowakowska, J. Szumera, K. Chwialkowska, I. Szarejko
2012 Plant Physiology  
to root hair genomics in a single, curated, and expandable database that is freely available at  ...  The database integrates bioinformatics tools with a focus on sequence identification and annotation. iRootHair is a unique resource for root hair research that integrates the large volume of data related  ...  ACKNOWLEDGMENTS We thank Agnieszka Janiak for the revision of the database and helpful comments and Paweł Sega, who helped to create the graphical models of the root hair mutants.  ... 
doi:10.1104/pp.112.206441 pmid:23129204 pmcid:PMC3532259 fatcat:vhlpeg3wsrgjnkr6ann3hd7p7m

Comparison Of Popular Bioinformatics Databases

Abdulganiyu Abdu Yusuf, Zahraddeen Sufyanu, Kabir Yusuf Mamman, Abubakar Umar Suleiman
2016 Zenodo  
The key features of the databases are demonstrated and detailed comparisons of the databases were made based on primary and secondary form of databases, and their uniqueness were also highlighted.  ...  They are GenBank, Protein Information Resource (PIR), DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL), Protein Data Bank (PDB), Universal Protein Resource (UniProt), Swiss-Prot  ...  (ii) In order to make the data comprehensive and authoritative, some important primary databases will exchange data every day through Internet, while secondary databases cannot exchange data in most cases  ... 
doi:10.5281/zenodo.154757 fatcat:t3jt4miscvhnjoixghtpdyw63m

How helpful are the protein-protein interaction databases and which ones? [article]

Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K Acharya
2019 bioRxiv   pre-print
In fact, a comprehensive list of such bioinformatics resources has not been reported so far.  ...  For the second approach, the back-end-data from the databases was downloaded and compared.  ...  Acknowledgements The authors thank colleagues at BdataA and Shodhaka Life Sciences Pvt. Ltd. for assistance in gathering some of the PPI data and analysis.  ... 
doi:10.1101/566372 fatcat:f46uga34djaarbpao2wgvzldu4

KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions

X.-w. Chen, J. C. Jeong, P. Dermyer
2010 Nucleic Acids Research  
Each data set is built from the overall database, which includes 185 446 IPPs and 1.5 billion NIPs from five primary databases: IntAct, HPRD, MINT, UniProt and the Gene Ontology.  ...  Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets.  ...  In the GRIP, IPPs are extracted from the MIPS Comprehensive Yeast Genome Database (8) , which includes only proteins in the same complex.  ... 
doi:10.1093/nar/gkq943 pmid:20952400 pmcid:PMC3013794 fatcat:yjsdiwxqrrc6jbpgzcyb4afjzi

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Tilmann Weber, Hyun Uk Kim
2016 Synthetic and Systems Biotechnology  
ClustScan was used to compile and analyze the data contained in the ClustScan database (see below).  ...  Table 1 1 Comprehensive collection of freely accessible software programs and databases dedicated to natural product research.  ... 
doi:10.1016/j.synbio.2015.12.002 pmid:29062930 pmcid:PMC5640684 fatcat:6hbbrigasjakrorunrhwymkmwe

PhenoHM: human–mouse comparative phenome–genome server

Divya Sardana, Suresh Vasa, Nishanth Vepachedu, Jing Chen, Ranga Chandra Gudivada, Bruce J. Aronow, Anil G. Jegga
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We acknowledge the help of Ron Bryson, Technical Writer, Division of Biomedical Informatics, CCHMC, OH, USA, in editing the article.  ...  EuroPhenome (28), a comprehensive resource for raw and annotated high-throughput phenotyping data].  ...  depth as available in the source databases and data compatibility.  ... 
doi:10.1093/nar/gkq472 pmid:20507906 pmcid:PMC2896149 fatcat:trb2tkybvvedrasjh6ob6j7a4e

Deletion of Immunoproteasome Subunits Imprints on the Transcriptome and Has a Broad Impact on Peptides Presented by Major Histocompatibility Complex I molecules

Danielle de Verteuil, Tara L. Muratore-Schroeder, Diana P. Granados, Marie-Hélène Fortier, Marie-Pierre Hardy, Alexandre Bramoullé, Étienne Caron, Krystel Vincent, Sylvie Mader, Sébastien Lemieux, Pierre Thibault, Claude Perreault
2010 Molecular & Cellular Proteomics  
Regulated genes segregated in clusters that were enriched in chromosomes 4 and 8.  ...  Molecular & Cellular Proteomics 9:2034 -2047, 2010.  ...  The list of MIPs reported in the present work has been provided to The Immune Epitope Database and Analysis Resource (http://beta.immuneepitope. org/) (36) .  ... 
doi:10.1074/mcp.m900566-mcp200 pmid:20484733 pmcid:PMC2938112 fatcat:ydncf4hgxjcttcja23x2anta5u

The Transporter Classification Database

Milton H. Saier, Vamsee S. Reddy, Dorjee G. Tamang, Åke Västermark
2013 Nucleic Acids Research  
This manuscript describes an update of the database descriptions previously featured in NAR database issues.  ...  Proteins in TCDB are organized in a five level hierarchical system, where the first two levels are the class and subclass, the second two are the family and subfamily, and the last one is the transport  ...  OTHER TRANSPORT DATABASES Only TCDB is comprehensive, including transport systems from all living organisms, and only TCDB has been adopted by the IUBMB.  ... 
doi:10.1093/nar/gkt1097 pmid:24225317 pmcid:PMC3964967 fatcat:szr7asdcf5a3ffkvdx6dniqhgy

HELP: The Herschel Extragalactic Legacy Project [article]

R. Shirley, K. Duncan, M.C. Campos Varillas, P.D. Hurley, K. Malek, Y. Roehlly, M.W.L. Smith, H. Aussel, T. Bakx, V. Buat, D. Burgarella, N. Christopher (+20 others)
2021 arXiv   pre-print
This project collates, curates, homogenises, and creates derived data products for most of the premium multi-wavelength extragalactic data sets.  ...  We also provide tools to access and analyse the full HELP database.  ...  We provide comprehensive meta data describing the data, using Virtual Observatory (VO) standards.  ... 
arXiv:2105.05659v1 fatcat:tn5ayhyy4ze25f2k5jkcbx56wq

Bioinformatic approaches to the study of Chlamydial diseases

X Rabasseda, S A Morré, S Ouburg
2009 Drugs of today  
Specialized chlamydia databases and analysis programs and the information they contain provide the opportunity for understanding and identifying key processes and phenomena associated with the unique infection  ...  in terms of established facts and in prediction models based on simulations, and therefore can greatly contribute to the development of potential new therapeutic approaches.  ...  ACKNOWLEDGMENTS The aims of this work are in part in line with the European EpiGenChlamydia Consortium which is supported by the European Commission within the Sixth Framework Programme through contract  ... 
pmid:20011711 fatcat:kkyga3ognfdxhj5r74jchnosfq

Understanding Tools and Techniques in Protein Structure Prediction [chapter]

Geraldine Sandana Mala John, Chellan Rose, Satoru Takeuchi
2011 Systems and Computational Biology - Bioinformatics and Computational Modeling  
et al., 2010) .  ...  In general, protein databases may be classified as Primary and Secondary databases, composite protein pattern databases and structure classification databases.  ... 
doi:10.5772/18585 fatcat:hxcc7ifyobedba3v7ptqrbzlhi

Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters

V. A. Benedito, H. Li, X. Dai, M. Wandrey, J. He, R. Kaundal, I. Torres-Jerez, S. K. Gomez, M. J. Harrison, Y. Tang, P. X. Zhao, M. K. Udvardi
2009 Plant Physiology  
The data presented here are a unique resource for the selection and functional characterization of legume transporters.  ...  Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots  ...  in comprehensive databases, and homology to classified TCDB transporters.  ... 
doi:10.1104/pp.109.148684 pmid:20023147 pmcid:PMC2832251 fatcat:oqsc4enrnjcqxc7wdcpeujr4na

The Arabidopsis genome: A foundation for plant research

M. Bevan
2005 Genome Research  
Acknowledgments We thank Przemek Prusinkiewicz, Enrico Coen, and colleagues for Figure 2 . This work was funded by the Core Strategic Grant to  ...  This method has been successfully implemented by the PlaNet database Consortium (Wilkinson et al. 2005) , who provide a comprehensive array of Arabidopsis genome-related data resources through BioMOBY  ...  This vast amount of information is not able to be captured by manual curation strategies alone, thus these data are fragmented, dispersed, and buried in the literature.  ... 
doi:10.1101/gr.3723405 pmid:16339360 fatcat:htkw4ypo6nfcfbqpjvadshazqu

Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections

Sapan Mandloi, Saikat Chakrabarti
2017 F1000Research  
UniProt Consortium: The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010; 38(Database issue): D142-8. PubMed Abstract | Publisher Full Text | Free Full Text 41.  ...  Data Source  ...  Inverse COVariance method (PSICOV program 23 ), from 753 curated protein family alignments, available from the Conserved Domain Database (CDD 36 ).  ... 
doi:10.12688/f1000research.11251.1 pmid:28751967 pmcid:PMC5506539 fatcat:xq7sxc3xwjdyrckruoq2fp6fka
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