GALA, a database for genomic sequence alignments and annotations

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

doi:10.1101/gr.603103

GALA, a database for genomic sequence alignments and annotations

Belinda Giardine, Laura Elnitski, Cathy Riemer, Izabela Makalowska, Scott Schwartz, Webb Miller, Ross C. Hardison

Research output: Contribution to journal › Review article › peer-review

43 Scopus citations

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/.

Original language	English (US)
Pages (from-to)	732-741
Number of pages	10
Journal	Genome research
Volume	13
Issue number	4
DOIs	https://doi.org/10.1101/gr.603103
State	Published - Apr 1 2003

All Science Journal Classification (ASJC) codes

Genetics
Genetics(clinical)

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10.1101/gr.603103

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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/.",

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AU - Giardine, Belinda

AU - Elnitski, Laura

AU - Riemer, Cathy

AU - Makalowska, Izabela

AU - Schwartz, Scott

AU - Miller, Webb

AU - Hardison, Ross C.

PY - 2003/4/1

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N2 - 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/.

AB - 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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GALA, a database for genomic sequence alignments and annotations

Abstract

All Science Journal Classification (ASJC) codes

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