A cross-species alignment tool (CAT)

doi:10.1186/1471-2105-8-349

	A cross-species alignment tool (CAT)
	Li, Heng ; Guan, Liang ; Liu, Tao ; Guo, Yiran ; Zheng, Wei-Mou ; Wong, Gane Ka-Shu ; Wang, Jun
	2007-09-19
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	8 页码:8
摘要	Background: The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences. Results: Here we present a new algorithm called CAT ( for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at http://xat.sourceforge.net/. Conclusions: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and sim4, with the sensitivity of the best inter-species tools, like GeneWise.
DOI	10.1186/1471-2105-8-349
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000251410100001
出版者	BIOMED CENTRAL LTD
引用统计	被引频次：4[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11053
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zheng, Wei-Mou
作者单位	1.Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China 2.Zhejiang Univ, James D Watson Inst Genome Sci, Hangzhou 310008, Peoples R China 3.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 4.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China 5.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China 6.Univ Washington, Dept Med, UW Genome Ctr, Seattle, WA 98195 USA 7.Univ Aarhus, Inst Human Genet, DK-8000 Aarhus, Denmark 8.Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense, Denmark
推荐引用方式 GB/T 7714	Li, Heng,Guan, Liang,Liu, Tao,et al. A cross-species alignment tool (CAT)[J]. BMC BIOINFORMATICS,2007,8:8.
APA	Li, Heng.,Guan, Liang.,Liu, Tao.,Guo, Yiran.,Zheng, Wei-Mou.,...&Wang, Jun.(2007).A cross-species alignment tool (CAT).BMC BIOINFORMATICS,8,8.
MLA	Li, Heng,et al."A cross-species alignment tool (CAT)".BMC BIOINFORMATICS 8(2007):8.