Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
Nucleic Acids Res
; 33(Database issue): D466-70, 2005 Jan 01.
Article
en En
| MEDLINE
| ID: mdl-15608239
ABSTRACT
We describe improvements to two databases that give access to information on genomic sequence similarities, functional elements in DNA and experimental results that demonstrate those functions. GALA, the database of Genome ALignments and Annotations, is now a set of interlinked relational databases for five vertebrate species, human, chimpanzee, mouse, rat and chicken. For each species, GALA records pairwise and multiple sequence alignments, scores derived from those alignments that reflect the likelihood of being under purifying selection or being a regulatory element, and extensive annotations such as genes, gene expression patterns and transcription factor binding sites. The user interface supports simple and complex queries, including operations such as subtraction and intersections as well as clustering and finding elements in proximity to features. dbERGE II, the database of Experimental Results on Gene Expression, contains experimental data from a variety of functional assays. Both databases are now run on the DB2 database management system. Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http//www.bx.psu.edu/.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Alineación de Secuencia
/
Genómica
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Bases de Datos de Ácidos Nucleicos
Límite:
Animals
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Humans
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2005
Tipo del documento:
Article
País de afiliación:
Estados Unidos