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EMBL Nucleotide Sequence Database in 2006

T. Kulikova, R. Akhtar, P. Aldebert, N. Althorpe, M. Andersson, A. Baldwin, K. Bates, S. Bhattacharyya, L. Bower, P. Browne, M. Castro, G. Cochrane (+22 others)
2007 Nucleic Acids Research  
The EMBL Nucleotide Sequence Database (http:// www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying  ...  Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. In 2006, the volume of data has continued to grow exponentially.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by EMBL. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl913 pmid:17148479 pmcid:PMC1897316 fatcat:jl52ytzxgjfbdlfnkny3vz7mci

EMBL Nucleotide Sequence Database: developments in 2005

G. Cochrane
2006 Nucleic Acids Research  
The EMBL Nucleotide Sequence Database (www.ebi. ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely  ...  Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by EMBL. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkj130 pmid:16381823 pmcid:PMC1347492 fatcat:2rpnnhv3ljhznmn2qe5gjgfhiq

IMGT/LIGM-DB, the IMGT(R) comprehensive database of immunoglobulin and T cell receptor nucleotide sequences

V. Giudicelli
2006 Nucleic Acids Research  
IMGT/LIGM-DB is the IMGT Õ comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species.  ...  IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases.  ...  IMGT/LIGM-DB DATA SOURCE AND CONTENT The unique source of IMGT/LIGM-DB nucleotide sequences is EMBL (14) .  ... 
doi:10.1093/nar/gkj088 pmid:16381979 pmcid:PMC1347451 fatcat:t3ete7g72rcmtncupigehq7cea

euHCVdb: the European hepatitis C virus database

C. Combet, N. Garnier, C. Charavay, D. Grando, D. Crisan, J. Lopez, A. Dehne-Garcia, C. Geourjon, E. Bettler, C. Hulo, P. L. Mercier, R. Bartenschlager (+7 others)
2007 Nucleic Acids Research  
A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses.  ...  As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses  ...  the EMBL nucleotide sequence database (8) and maintained in the PostgreSQL relational database management system (RDMS).  ... 
doi:10.1093/nar/gkl970 pmid:17142229 pmcid:PMC1669729 fatcat:wuqj36vx6bhknd6khtepveam2m

From metaphor to practices: The introduction of "information engineers" into the first DNA sequence database

Miguel García-Sancho
2011 History and Philosophy of the Life Sciences  
in practices and professionals such as those incorporated at the EMBL.  ...  This paper explores the introduction of professional systems engineers and information management practices into the first centralized DNA sequence database, developed at the European Molecular Biology  ...  Stueber (1983) , "EMBL Nucleotide Sequence Data Library User Manual" in G. Cameron personal archive, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK.  ... 
pmid:21789956 fatcat:5qezrlvlqzg5rchzliemw6imnu

Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics

Satoshi Tamaki, Kazuharu Arakawa, Nobuaki Kono, Masaru Tomita
2007 Genomics, Proteomics & Bioinformatics  
Sequences submitted to the International Nucleotide Sequence Database Collaboration (INSDC) through GenBank (2 ) , the European Molecular Biology Laboratory (EMBL) (3 ) , and the DNA Data Bank of Japan  ...  : AL009126 07-JUL-2003 (rel. 76, ver. 3); E. coli-EMBL: U00096 13-AUG-2006 (rel. 88, ver. 6); M. genitalium-EMBL: L43967 14-JAN-2006 (rel. 86, ver. 2); M. tuberculosis-EMBL: AE000516 14-APR-2005 (rel.  ...  NK developed the web database and edited the manuscript. MT supervised the research and revised the final manuscript. All authors read and approved the final manuscript.  ... 
doi:10.1016/s1672-0229(07)60014-x pmid:17572364 pmcid:PMC5054091 fatcat:efpsmyyxtrhwba4r2b4366jeze

Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration

Hallam Stevens
2017 Journal of the History of Biology  
This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database  ...  The technical and social groundwork for the international exchange of nucleotide sequences created the conditions of possibility for imagining nucleotide sequences (and subsequently genomes) as a "global  ...  The National Institute of Genetics in Mishima, Japan also provided support that enabled me to present a version of this paper there.  ... 
doi:10.1007/s10739-017-9490-y pmid:28986915 fatcat:panniideznbnhfelfspeygb6v4

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA [article]

Michael Gruenstaeudl
2019 bioRxiv   pre-print
Motivation: The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research.  ...  As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.  ...  INTRODUCTION The submission of nucleotide sequence data to public sequence databases is a central pillar in the academic effort to share scientific data and make biological research more reproducible  ... 
doi:10.1101/820480 fatcat:wjff5l5ieze4fmemkppdcz53ne

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees

S. Whelan
2006 Nucleic Acids Research  
PANDIT is a database of homologous sequence 10 alignments accompanied by estimates of their corresponding phylogenetic trees.  ...  Currently in version 17.0, PANDIT com-15 prises 7738 families of homologous protein domains; for each family, DNA and corresponding amino acid sequence multiple alignments are available together with high  ...  To retrieve DNA for the protein sequences in PANDIT-aa, 40 cross-references to the EMBL Nucleotide Sequence Database (15) are obtained from the SWISS-PROT and TrEMBL databases that are now incorporated  ... 
doi:10.1093/nar/gkj087 pmid:16381879 pmcid:PMC1347450 fatcat:67crnugkrbc3ldkdfcckleutpu

Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare

Takushi Toda, Kinya Toriyama
2013 Rice  
Nucleotides of the discrepant sites were all identical to those in DQ167400.1. The sequence in BA000029.3 is thought to contain sequencing errors.  ...  Conclusion: Nucleotide sequences of the mitochondrial genes in BA000029.3 need to be updated using the data in this study when used as a reference genome.  ...  Acknowledgments This work was supported by a Grant-in-Aid (Nos.2338002 and 24117502) from the Ministry of Education, Science, Sports and Culture, Japan.  ... 
doi:10.1186/1939-8433-6-2 pmid:24280589 pmcid:PMC5394982 fatcat:qzpiy7x45jgslair3m2bcfca6q

GenBank

D. A. Benson
2006 Nucleic Acids Research  
Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage.  ...  BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.  ...  GenBank CON records for assemblies of smaller records In 1995, the DDBJ/EMBL/GenBank International Nucleotide Sequence Collaboration Databases agreed to a 350 kb limit on the size of most database sequence  ... 
doi:10.1093/nar/gkj157 pmid:16381837 pmcid:PMC1347519 fatcat:m6y3phyjrjbttfr52zgdzv5q5e

Biological Data Resources at the EMBL-EBI

Rodrigo Lopez
2008 Revista Colombiana de Biotecnología  
The EBI has been maintaining core data resources in molecular biology for 15 years and is notionally custodian to the largest collection of databases and services in Life Sciences in Europe.  ...  The European Bioinformatics Institute (EBI) is an Outstation of the European Molecular Biology Laboratory (EMBL).  ...  This database is part of INSDC (International Nucleotide Sequence Database Collaboration (see: www.insdc.org), which is composed of the National Centre of Biotechnology Information (NCBI) in the United  ... 
doaj:1181789ff05043988701f7c984425c83 fatcat:aoqiuavzcreutlry6vbuzaoxhm

Taura syndrome virus from Penaeus vannamei shrimp cultured in Korea

JW Do, SJ Cha, NS Lee, YC Kim, JW Kim, JD Kim, JW Park
2006 Diseases of Aquatic Organisms  
The nucleotide sequences of the partial capsid protein VP1 of 2 Korean isolates were 99% identical to each other and 96 to 99% identical to those of TSVs isolated from the Americas, Taiwan, and Thailand  ...  Mass mortality occurred among Penaeus vannamei shrimp cultured in Korea in 2004.  ...  The nucleotide sequences were compared with the GenBank/EMBL databases using BLAST.  ... 
doi:10.3354/dao070171 pmid:16875405 fatcat:3dm57acbhfcatgg6bg5slllrlu

DPVweb: a comprehensive database of plant and fungal virus genes and genomes

M. J. Adams
2006 Nucleic Acids Research  
Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format.  ...  The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently  ...  We thank the AAB for their support, in particular by funding the development of the standalone DPV program and for sponsoring the DPVweb internet site.  ... 
doi:10.1093/nar/gkj023 pmid:16381892 pmcid:PMC1347386 fatcat:jazyxyxymjbxrauc7ruqrqawty

Hepatitis C databases, principles and utility to researchers

Carla Kuiken, Masashi Mizokami, Gilbert Deleage, Karina Yusim, Francois Penin, Tadasu Shin-I, Céline Charavay, Ning Tao, Daniel Crisan, Delphine Grando, Anita Dalwani, Christophe Geourjon (+2 others)
2006 Hepatology  
The HCV database at the Los Alamos National Laboratory in the United States (http://hcv.lanl.gov) provides access to a manually annotated sequence database and a database of immunological epitopes which  ...  In this paper, we briefly describe each of these databases and their associated websites and tools, and give some examples of their use in furthering HCV research.  ...  Acknowledgment: The Los Alamos HCV database project is deeply indebted to the Los Alamos HIV database group, led by Dr.  ... 
doi:10.1002/hep.21162 pmid:16628639 fatcat:x4ej3hydbnhzhfobzmief46a7m
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