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Vol 13, Issue 4, 732-741, April 2003

RESOURCES

GALA, a Database for Genomic Sequence Alignments and Annotations

Belinda Giardine1, Laura Elnitski1,2, Cathy Riemer1, Izabela Makalowska4, Scott Schwartz1, Webb Miller1,3,4 and Ross C. Hardison2,4,5

Departments of 1Computer Science and Engineering,2 Biochemistry and Molecular Biology, 3Biology, and4 Huck Institute for Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

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/.

5 Corresponding author.

E-MAIL rch8{at}psu.edu; FAX (814) 863-7024.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.603103.


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