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题名: A cross-species alignment tool (CAT)
作者: Li, Heng ;  Guan, Liang ;  Liu, Tao ;  Guo, Yiran ;  Zheng, Wei-Mou ;  Wong, Gane Ka-Shu ;  Wang, Jun
刊名: BMC BIOINFORMATICS
出版日期: 2007
卷号: 8, 期号:1, 页码:-
关键词: GENOMIC DNA ;  ANNOTATION ;  SEQUENCES ;  PROGRAMS ;  DATABASE ;  SEARCH ;  BLAST
学科分类: Physics
通讯作者: Zheng, WM , Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China
部门归属: Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China; Zhejiang Univ, James D Watson Inst Genome Sci, Hangzhou 310008, Peoples R China; Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China; Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China; Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China; Univ Washington, Dept Med, UW Genome Ctr, Seattle, WA 98195 USA; Univ Aarhus, Inst Human Genet, DK-8000 Aarhus, Denmark; Univ So Denmark, Dept Biochem & Mol Biol, DK-5230 Odense, Denmark
英文摘要: 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.
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000251410100001
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/5659
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

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Li, Heng,Guan, Liang,Liu, Tao,et al. A cross-species alignment tool (CAT)[J]. BMC BIOINFORMATICS,2007,8(1):-.
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