GALA, a database for genomic sequence alignments and annotations

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

Research output: Contribution to journalReview article

43 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)732-741
Number of pages10
JournalGenome research
Volume13
Issue number4
DOIs
StatePublished - Apr 1 2003

Fingerprint

Sequence Alignment
Databases
Genes
CpG Islands
Globins
Conserved Sequence
Single Nucleotide Polymorphism
Genome

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Giardine, B., Elnitski, L., Riemer, C., Makalowska, I., Schwartz, S., Miller, W., & Hardison, R. C. (2003). GALA, a database for genomic sequence alignments and annotations. Genome research, 13(4), 732-741. https://doi.org/10.1101/gr.603103
Giardine, Belinda ; Elnitski, Laura ; Riemer, Cathy ; Makalowska, Izabela ; Schwartz, Scott ; Miller, Webb ; Hardison, Ross Cameron. / GALA, a database for genomic sequence alignments and annotations. In: Genome research. 2003 ; Vol. 13, No. 4. pp. 732-741.
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Giardine, B, Elnitski, L, Riemer, C, Makalowska, I, Schwartz, S, Miller, W & Hardison, RC 2003, 'GALA, a database for genomic sequence alignments and annotations', Genome research, vol. 13, no. 4, pp. 732-741. https://doi.org/10.1101/gr.603103

GALA, a database for genomic sequence alignments and annotations. / Giardine, Belinda; Elnitski, Laura; Riemer, Cathy; Makalowska, Izabela; Schwartz, Scott; Miller, Webb; Hardison, Ross Cameron.

In: Genome research, Vol. 13, No. 4, 01.04.2003, p. 732-741.

Research output: Contribution to journalReview article

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AU - Giardine, Belinda

AU - Elnitski, Laura

AU - Riemer, Cathy

AU - Makalowska, Izabela

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AU - Miller, Webb

AU - Hardison, Ross Cameron

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Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W et al. GALA, a database for genomic sequence alignments and annotations. Genome research. 2003 Apr 1;13(4):732-741. https://doi.org/10.1101/gr.603103