GALA, a Database for Genomic Sequence Alignments and Annotations | Zendy

Belinda Giardine | Zendy; Laura Elnitski | Zendy; Cathy Riemer | Zendy; Izabela Makałowska | Zendy; Scott Schwartz | Zendy; Webb Miller | Zendy; Ross C. Hardison | Zendy

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GALA, a Database for Genomic Sequence Alignments and Annotations

Author(s) -

Belinda Giardine,

Laura Elnitski,

Cathy Riemer,

Izabela Makałowska,

Scott Schwartz,

Webb Miller,

Ross C. Hardison

Publication year - 2003

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.603103

Subject(s) - biology , genome , genetics , gene , cpg site , human genome , sequence (biology) , computational biology , conserved sequence , sequence alignment , database , base sequence , dna methylation , peptide sequence , gene expression , computer science

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/.

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