| URL: | http://gala.bx.psu.edu/ |
| Full name: | Genome ALignments and Annotations |
| Description: | 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. |
| Year founded: | 2003 |
| Last update: | 2009-01-09 |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | United States |
| Data type: | |
| Data object: |
NA
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| Database category: | |
| Major species: |
NA
|
| Keywords: |
| University/Institution: | Pennsylvania State University |
| Address: | University Park, PA 16802, USA |
| City: | University Park |
| Province/State: | PA |
| Country/Region: | United States |
| Contact name (PI/Team): | Ross C. Hardison |
| Contact email (PI/Helpdesk): | rch8@psu.edu |
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Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. [PMID: 15608239]
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/. |
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GALA, a database for genomic sequence alignments and annotations. [PMID: 12671007]
We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/. |