GALA (Genome Alignment and Annotation Database) combines genomic annotation data with multi-species alignments to allow powerful querying on publicly available sequence information.
It incorporates diverse annotation information including genes, expression levels, disease association, SNPs, binding sites, sequence conservation, regulatory potential, and more, from multiple sources such as GenBank, Ensembl, the UCSC Genome Browser, and local computation.
One of GALA's special strengths is the ability to search based on regions' relative positions. For example, one can query on characteristics involving distal loci (e.g. the level of sequence conservation upstream of a selected gene), or based on proximity (e.g. SNP density that is higher than expected).
Users can formulate simple queries using any field in the database individually, and can combine these results to refine and narrow the scope of the inquiry. A History page keeps track of each user's queries, and provides various operations for combining them to construct more complex ones. Several options are provided for textual output or visualization of the results, including displaying them as a custom user track at the UCSC Genome Browser.
Publications:
GALA, a database for genomic sequence alignments and annotations.
Belinda Giardine, Laura Elnitski, Cathy Riemer, Izabela Makalowska,
Scott Schwartz, Webb Miller, and Ross C. Hardison
Genome Research Vol. 13, Issue 4, 732-741, April 2003
PubMed