GALA, a Database for Genomic Sequence Alignments and Annotations
Open Access
- 1 April 2003
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 13 (4) , 732-741
- https://doi.org/10.1101/gr.603103
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 athttp://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.Keywords
This publication has 34 references indexed in Scilit:
- Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian EvolutionGenome Research, 2003
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- The Origin Recognition Complex Marks a Replication Origin in the Human TOP1 Gene PromoterJournal of Biological Chemistry, 2002
- The Human Genome Browser at UCSCGenome Research, 2002
- Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams SyndromeGenome Research, 2002
- The HUGO Gene Nomenclature Committee (HGNC)Human Genetics, 2001
- Initial sequencing and analysis of the human genomeNature, 2001
- Comparative Sequence Analysis of the Mouse and Human Lgn1/SMA IntervalGenomics, 1999
- Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology, 1997
- Evolutionary Strategies for the Elucidation ofcisandtransFactors That Regulate the Developmental Switching Programs of the β-like Globin GenesMolecular Phylogenetics and Evolution, 1996