title: GALA, a database for genomic sequence alignments and annotations.
abstract: 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/.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Belinda
authors.initials: B
authors.lastname: Giardine
authors.forename: Laura
authors.initials: L
authors.lastname: Elnitski
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Izabela
authors.initials: I
authors.lastname: Makalowska
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D018899:CpG Islands / Q000235:genetics; D030541:Databases, Genetic; D005807:Genes, Overlapping / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D020121:5' Untranslated Regions