Biomaterial Database

Remote access to ACNUC nucleotide and protein sequence databases at PBIL. 2008

Manolo Gouy, and Stéphane Delmotte

Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69622 Villeurbanne Cedex, France. mgouy@biomserv.univ-lyon1.fr

The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pôle Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query_win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/acnuc/acnuc.html).

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D003628	Database Management Systems	Software designed to store, manipulate, manage, and control data for specific uses.	Data Base Management Systems,Management System, Data Base,Management Systems, Data Base,System, Data Base Management,Systems, Data Base Management,Database Management System
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D012984	Software	Sequential operating programs and data which instruct the functioning of a digital computer.	Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software
D014584	User-Computer Interface	The portion of an interactive computer program that issues messages to and receives commands from a user.	Interface, User Computer,Virtual Systems,User Computer Interface,Interface, User-Computer,Interfaces, User Computer,Interfaces, User-Computer,System, Virtual,Systems, Virtual,User Computer Interfaces,User-Computer Interfaces,Virtual System
D017422	Sequence Analysis, DNA	A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.	DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D019295	Computational Biology	A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.	Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D020407	Internet	A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.	World Wide Web,Cyber Space,Cyberspace,Web, World Wide,Wide Web, World
D030561	Databases, Nucleic Acid	Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.	DDBJ,DNA Data Bank of Japan,DNA Data Banks,DNA Databases,Databases, DNA,Databases, DNA Sequence,Databases, Nucleic Acid Sequence,Databases, RNA,Databases, RNA Sequence,EMBL Nucleotide Sequence Database,GenBank,Nucleic Acid Databases,RNA Databases,DNA Databanks,DNA Sequence Databases,European Molecular Biology Laboratory Nucleotide Sequence Database,Nucleic Acid Sequence Databases,RNA Sequence Databases,Bank, DNA Data,Banks, DNA Data,DNA Data Bank,DNA Databank,DNA Database,DNA Sequence Database,Data Bank, DNA,Data Banks, DNA,Databank, DNA,Databanks, DNA,Database, DNA,Database, DNA Sequence,Database, Nucleic Acid,Database, RNA,Database, RNA Sequence,Nucleic Acid Database,RNA Database,RNA Sequence Database,Sequence Database, DNA,Sequence Database, RNA,Sequence Databases, DNA,Sequence Databases, RNA
D030562	Databases, Protein	Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.	Amino Acid Sequence Databases,Databases, Amino Acid Sequence,Protein Databases,Protein Sequence Databases,SWISS-PROT,Protein Structure Databases,SwissProt,Database, Protein,Database, Protein Sequence,Database, Protein Structure,Databases, Protein Sequence,Databases, Protein Structure,Protein Database,Protein Sequence Database,Protein Structure Database,SWISS PROT,Sequence Database, Protein,Sequence Databases, Protein,Structure Database, Protein,Structure Databases, Protein