Remote access to ACNUC nucleotide and protein sequence databases at PBIL
Autor: | Manolo Gouy, Stéphane Delmotte |
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Přispěvatelé: | Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) |
Rok vydání: | 2008 |
Předmět: |
Protein structure database
Computer science Molecular Sequence Data computer.software_genre Biochemistry User-Computer Interface 03 medical and health sciences RefSeq Humans Ensembl [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Databases Protein 030304 developmental biology nucleotide sequence database Internet 0303 health sciences Sequence profiling tool Database Sequence database Application programming interface 030302 biochemistry & molecular biology Computational Biology Sequence Analysis DNA bioinformatics General Medicine database retrieval [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ACNUC ComputingMethodologies_PATTERNRECOGNITION GenBank Database Management Systems UniProt Databases Nucleic Acid computer Software |
Zdroj: | Biochimie Biochimie, Elsevier, 2008, 90 (4), pp.555-562. ⟨10.1016/j.biochi.2007.07.003⟩ Biochimie, 2008, 90 (4), pp.555-562. ⟨10.1016/j.biochi.2007.07.003⟩ |
ISSN: | 0300-9084 |
DOI: | 10.1016/j.biochi.2007.07.003 |
Popis: | 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). |
Databáze: | OpenAIRE |
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