Conservation, regulation, synteny, and introns in a large-scale C-briggsae-C-elegans genomic alignment
Conservation, regulation, synteny, and introns in a large-scale C-briggsae-C-elegans genomic alignment
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DOI：
10.1101/gr.10.8.1115
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发表时间：
2000-08-01
期刊：
影响因子：
7
通讯作者：
Zahler, AM
中科院分区：
文献类型：
--
作者：
Kent, WJ;Zahler, AM
开发了一种新的算法WABA，用于在不同物种的基因组DNA之间进行大规模比对。WABA用于将800万个碱基的秀丽隐杆线虫基因组DNA与9700万个碱基的秀丽隐杆线虫基因组进行比对。该比对包括154个具有遗传特征的秀丽隐杆线虫基因的C. briggsae同源物，以及许多倍于此数量的大部分未表征的orf，可以在网上浏览和搜索（http://www.cse.ucsc.edu/similar to kent/intronerator）。比对证实了保守模式在识别调控区和很少表达的编码区是有用的。保守的调控元件可以通过检查密码子摆动位置的发散水平来识别编码外显子。排列结果显示同工区大小呈双峰分布。在一个物种中有超过250个内含子，而在另一个物种中没有。同一物种特有的内含子的3‘和5’剪接位点之间的相似性高于线虫内含子的整体剪接位点，这提示了内含子去除的可能机制。
A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 genetically characterized C. elegans genes and many times this number of largely uncharacterized ORFs, can be browsed and searched on the Web (http://www.cse.ucsc.edu/similar to kent/intronerator). The alignment confirms that patterns of conservation can be useful in identifying regulatory regions and rarely expressed coding regions. Conserved regulatory elements can be identified inside coding exons by examining the level of divergence at the wobble position of codons. The alignment reveals a bimodal size distribution of syntenic regions. Over 250 introns are present in one species but not the other. The 3' and 5' intron splice sites have more similarity to each other in introns unique to one species than in C. elegans introns as a whole, suggesting a possible mechanism for intron removal.