title: Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
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/.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA. llb111@psu.edu
authors.forename: Laura
authors.initials: L
authors.lastname: Elnitski
authors.forename: Belinda
authors.initials: B
authors.lastname: Giardine
authors.forename: Prachi
authors.initials: P
authors.lastname: Shah
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Matthew
authors.initials: M
authors.lastname: Weirauch
authors.forename: Richard
authors.initials: R
authors.lastname: Burhans
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D051379:Mice; D002679:Pan troglodytes / Q000235:genetics; D051381:Rats; D016415:Sequence Alignment; D014584:User-Computer Interface