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The National Center for Biotechnology Information's Protein Clusters Database

William Klimke, Richa Agarwala, Azat Badretdin, Slava Chetvernin, Stacy Ciufo, Boris Fedorov, Boris Kiryutin, Kathleen O'Neill, Wolfgang Resch, Sergei Resenchuk, Susan Schafer, Igor Tolstoy (+1 others)
2008 Nucleic Acids Research  
The NCBI Protein Clusters Database (ProtClustDB) has been created to efficiently maintain and keep the deluge of data up to date.  ...  There are 7180 clusters containing 376 513 proteins with curated gene and protein functional annotation.  ...  For example, curation centered around clusters that contain Escherichia coli K-12 proteins includes information from curated databases such as EcoGene and EcoCyc (18, 19) .  ... 
doi:10.1093/nar/gkn734 pmid:18940865 pmcid:PMC2686591 fatcat:rtrzuma6ubb33i6gsivhsi7yca

Structure Based Protein Multiple Sequence Alignment Algorithm on a Parallel System

Muhammad Ishaq Afridi, Yin Gui Sheng
2012 International Journal of Machine Learning and Computing  
To enhance the speed and efficiency of structure based algorithms for protein Multiple Sequence alignment we need parallel processing.  ...  If we use a parallel computer cluster or Grid then we can reduce processing time and get an optimal result. It will predict the function of protein from its structure.  ...  Accession number can be found by performing BLASTP 3 (search protein database using a protein query) at NCBI (National center for biotechnology information) [18] , 1 An algorithm that Combine sequence  ... 
doi:10.7763/ijmlc.2012.v2.86 fatcat:wm6kclvy45aq5phq75pqzmx7s4

Enterovirus genotypes causing hand foot and mouth disease in Shanghai, China: a molecular epidemiological analysis

Menghua Xu, Liyun Su, Lingfeng Cao, Huaqing Zhong, Niuniu Dong, Jin Xu
2013 BMC Infectious Diseases  
Results: Of 290 specimens, 277 (95.5%) tested positive for enterovirus. The major genotypes were EV71 (63.8%), CA10 (9.0%), CA6 (8.3%), CA16 (6.9%), CA12 (2.4%), and CA4 (1.4%).  ...  Mean hospital stays and the prevalence of complications in patients with EV71 infection were higher than those in patients in CA6, CA10 or CA16 infection (P < 0.05 for all comparisons).  ...  Acknowledgements This work was supported by the Program for New Century Excellent Talents in University (NECT-09-0320) and supported by the Program for Excellent Academic Leaders in Public Health in Shanghai  ... 
doi:10.1186/1471-2334-13-489 pmid:24148902 pmcid:PMC4015791 fatcat:mtjvpoi425c5lgdblaxt4jkegu

Page 43 of None Vol. 50, Issue 6 [page]

2001 None  
A search of the National Center for Biotechnology Information’s human expressed sequence tag (EST) database for apo- bec-1-like cytidine deaminases containing the conserved signature sequence (H/C)-(A/  ...  Scanning the ARCD-1 protein sequence against the Pfam database (http://pfam.wustl.edu/) demonstrated the presence of the active site zinc-bind- ing domain between amino acids 98 and 131 (Fig. 3A) (5).  ... 

Development and characterization of EST ‐ SSR markers for Camellia reticulata

Yan Tong, Li‐Zhi Gao
2020 Applications in Plant Sciences  
We detected 4780 SSRs in C. reticulata from Camellia RNA-Seq data deposited in the National Center for Biotechnology Information's expressed sequence tags database (dbEST).  ...  for this species.  ...  DATA AVAILABILITY Expressed sequence tag sequences for the newly developed primers have been deposited to the National Center for Biotechnology Information (NCBI)'s GenBank database; accession numbers  ... 
doi:10.1002/aps3.11348 pmid:32477844 pmcid:PMC7249272 fatcat:cjtqft3nmrgwncpub3fnr72rgm

Comparative metagenomics of microbial traits within oceanic viral communities

Itai Sharon, Natalia Battchikova, Eva-Mari Aro, Carmela Giglione, Thierry Meinnel, Fabian Glaser, Ron Y Pinter, Mya Breitbart, Forest Rohwer, Oded Béjà
2011 The ISME Journal  
In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication.  ...  the already known transcription level control.  ...  contre le Cancer, Villejuif) grant 4920 (CG and TM), and grant DBI-0850206 from the National Science Foundation (MB).  ... 
doi:10.1038/ismej.2011.2 pmid:21307954 pmcid:PMC3146289 fatcat:rvjjzz3q2be6vm7c752x3zgpte

PartiGeneDB--collating partial genomes

J. M. Peregrin-Alvarez
2004 Nucleic Acids Research  
Users may query the database to identify particular genes of interest either on the basis of sequence similarity or via the use of simple text searches for specific patterns of BLAST annotation.  ...  For the most part, these data are poorly organized and difficult to analyse.  ...  Computational analyses were performed at the Center for Computational Biology, Hospital for Sick Children.  ... 
doi:10.1093/nar/gki109 pmid:15608203 pmcid:PMC540063 fatcat:g6mwdzvoijbdjlntyrsx5afj4y

CyanoBase: a large-scale update on its 20th anniversary

Takatomo Fujisawa, Rei Narikawa, Shin-ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai (+1 others)
2016 Nucleic Acids Research  
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http:// genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to  ...  Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary.  ...  Metadata and cross references CyanoBase also contains metadata associated with cyanobacterial genomes that have been collected from multiple sources, such as the National Center for Biotechnology Information's  ... 
doi:10.1093/nar/gkw1131 pmid:27899668 pmcid:PMC5210588 fatcat:rug7iheelffxvccvlbvzzqc5ze

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy

Tanja Bekhuis
2006 Biomedical Digital Libraries  
This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information.  ...  Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians  ...  For example, see the National Center for Biotechnology Information's catalog of resources [5] . These digital databases are information rich, but still relatively opaque without mining tools.  ... 
doi:10.1186/1742-5581-3-2 pmid:16584552 pmcid:PMC1459187 fatcat:43hj56ap6zd4jbr53vf5mwq7ra

Computational-based approaches in epigenetic research: Insights from computational tools, mathematical models, and machine learning methods

2019 Journal of Applied Biology & Biotechnology  
The methods implemented for this purpose must be able to handle massive data of experimental works and process the epigenetic layers.  ...  In this study, we briefly reviewed challenges in the way of the computational epigenetics, the latest reported methods, and significant biological results derived from applying computational-based methods  ...  Of other useful databases, we could mention to the Histone Database, ChromDB, CREMOFAC, the National Human Genome Research Institute's Histone Database, the National Center for Biotechnology Information's  ... 
doi:10.7324/jabb.2019.70114 fatcat:roy6zefzhzaaxnzilc6wtynnhi

Transcriptomics reveal the molecular underpinnings of chemosensory proteins in Chlorops oryzae

Lin Qiu, Shunjie Tao, Hualiang He, Wenbing Ding, Youzhi Li
2018 BMC Genomics  
Conclusions: The identification of chemosensory genes in C. oryzae provides a foundation for the investigation of the function of chemosensory proteins in this species, which, in turn, could allow the  ...  However, little is known about the chemosensory proteins of Chlorops oryzae, a major pest of rice crops throughout Asia.  ...  The raw data submitted to the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/) with the accession numbers of SRR7528441, SRR7528446, SRR7528467, SRR7529086, SRR7529100  ... 
doi:10.1186/s12864-018-5315-4 fatcat:jesaqodjpfaoncg4ihb5taqdzi

Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil: TABLE 1

Fernanda Almeida, Marta Inês Cazentini Medeiros, Dália Prazeres Rodrigues, Justin Payne, Ruth E. Timme, Marc W. Allard, Juliana Pfrimer Falcão
2016 Genome Announcements  
Salmonellosis is an important health problem worldwide and Salmonella enterica serovar Typhimurium is one of the most common isolated serovars. Here, we reported the draft genomes of 40 S .  ...  The National Center for Biotechnology Information's protein Clusters Database. Nucleic Acids Res 37:D216 -D223. http:// dx.doi.org/10.1093/nar/gkn734. 7.  ...  The genome length was also within the range described for Salmonella (4.6 Mb to almost 5.1 Mb) (8). The number of contigs per assembly for each isolate ranged from 47 to 286.  ... 
doi:10.1128/genomea.00892-16 pmid:27660768 pmcid:PMC5034119 fatcat:lrioeypxljauha3mcqleho3tqe

Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of group G M. aeruginosa

Haruyo Yamaguchi, Shigekatsu Suzuki, Yasunori Osana, Masanobu Kawachi
2018 Journal of Genomics  
strains, and the genomes do not contain a microcystin biosynthetic gene cluster in common.  ...  The complete genome sequence of M. aeruginosa NIES-2481 comprises a 4.29-Mbp circular chromosome and a 147,539-bp plasmid; the circular chromosome and the plasmid contain 4,332 and 167 protein-coding genes  ...  Acknowledgments This study was supported by the Japan Agency for Medical Research and Development (AMED).  ... 
doi:10.7150/jgen.24935 pmid:29576807 pmcid:PMC5865083 fatcat:25yniqkyavhknhonmnnczg6rq4

Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability

A. Marchetti, D. M. Schruth, C. A. Durkin, M. S. Parker, R. B. Kodner, C. T. Berthiaume, R. Morales, A. E. Allen, E. V. Armbrust
2012 Proceedings of the National Academy of Sciences of the United States of America  
Archibald generously provided EST databases for Geminigera cryophila (Hackett) and Guillardia theta (Archibald) used in our analysis.  ...  Tully for assistance during the cruise. We are grateful to J. Barwell-Clarke, K. Johnson, and N. Sutherland (Institute of Ocean Sciences) for sharing nutrients and iron data; F.  ...  The datasets examined were available marine eukaryotic genomes and ESTs, National Center for Biotechnology Information's EST database (excluded Fungi and Metazoa except Copepoda), and National Center for  ... 
doi:10.1073/pnas.1118408109 pmid:22308424 pmcid:PMC3277525 fatcat:pju6fi76cbavzgmypqfa5pfyfi

In search of genome annotation consistency: solid gene clusters and how to use them

James J. Davis, Gary J. Olsen, Ross Overbeek, Veronika Vonstein, Fangfang Xia
2013 3 Biotech  
We also compare SEED annotation consistencies with other commonly used resources such as IMG (the Joint Genome Institute's Integrated Microbial Genomes system), RefSeq (the National Center for Biotechnology  ...  Information's Reference Sequence Database), Swiss-Prot (the annotated protein sequence database of the Swiss Institute of Bioinformatics, European Molecular Biology Laboratory and the European Bioinformatics  ...  and the source are credited.  ... 
doi:10.1007/s13205-013-0152-2 pmid:28324432 pmcid:PMC4026451 fatcat:y4qen3wbpbgwxdiljmwjxvc5si
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