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GALA，一个用于基因组序列比对和注释的数据库。

GALA, a database for genomic sequence alignments and annotations.

作者信息

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

机构信息

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

出版信息

Genome Res. 2003 Apr;13(4):732-41. doi: 10.1101/gr.603103.

DOI:10.1101/gr.603103
PMID:12671007
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC430176/
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/.

摘要

我们开发了一个关系数据库，用于存储人类和小鼠之间的全基因组序列比对以及人类序列的广泛注释。支持对记录的特征进行复杂查询，包括直接查询以及基于它们之间的邻近关系进行查询。搜索可以揭示各种各样的关系，例如找到在指定组织中表达且在起始位点5'端具有高度保守非编码序列的所有基因。其他例子包括找到基因上游保守非编码区域中出现的单核苷酸多态性，以及识别与反向转录基因5'端重叠的CpG岛。该数据库可在http://globin.cse.psu.edu/和http://bio.cse.psu.edu/在线获取。

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本文引用的文献

1
Human-mouse alignments with BLASTZ.
Genome Res. 2003 Jan;13(1):103-7. doi: 10.1101/gr.809403.
2
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Genome Res. 2003 Jan;13(1):13-26. doi: 10.1101/gr.844103.
3
Initial sequencing and comparative analysis of the mouse genome.
Nature. 2002 Dec 5;420(6915):520-62. doi: 10.1038/nature01262.
4
A high-resolution recombination map of the human genome.
Nat Genet. 2002 Jul;31(3):241-7. doi: 10.1038/ng917. Epub 2002 Jun 10.
5
The human genome browser at UCSC.
Genome Res. 2002 Jun;12(6):996-1006. doi: 10.1101/gr.229102.
6
The origin recognition complex marks a replication origin in the human TOP1 gene promoter.
J Biol Chem. 2002 Aug 30;277(35):31430-40. doi: 10.1074/jbc.M202165200. Epub 2002 May 9.
7
The HUGO Gene Nomenclature Committee (HGNC).
Hum Genet. 2001 Dec;109(6):678-80. doi: 10.1007/s00439-001-0615-0. Epub 2001 Oct 24.
8
Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome.
Genome Res. 2002 Jan;12(1):3-15. doi: 10.1101/gr.214802.
9
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.
Nucleic Acids Res. 2002 Jan 1;30(1):52-5. doi: 10.1093/nar/30.1.52.
10
The Ensembl genome database project.
Nucleic Acids Res. 2002 Jan 1;30(1):38-41. doi: 10.1093/nar/30.1.38.

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