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A cross-species alignment tool (CAT)
Li, Heng; Guan, Liang; Liu, Tao; Guo, Yiran; Zheng, Wei-Mou; Wong, Gane Ka-Shu; Wang, Jun; Zheng, WM , Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China
2007
发表期刊BMC BIOINFORMATICS
ISSN1471-2105
卷号8期号:1页码:-
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.
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
关键词Genomic Dna Annotation Sequences Programs Database Search Blast
学科领域Physics
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收录类别SCI
WOS记录号WOS:000251410100001
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被引频次:2[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/5659
专题理论物理所1978-2010年知识产出
通讯作者Zheng, WM , Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China
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GB/T 7714
Li, Heng,Guan, Liang,Liu, Tao,et al. A cross-species alignment tool (CAT)[J]. BMC BIOINFORMATICS,2007,8(1):-.
APA Li, Heng.,Guan, Liang.,Liu, Tao.,Guo, Yiran.,Zheng, Wei-Mou.,...&Zheng, WM , Chinese Acad Sci, Beijing Inst Genom, Beijing 101300, Peoples R China.(2007).A cross-species alignment tool (CAT).BMC BIOINFORMATICS,8(1),-.
MLA Li, Heng,et al."A cross-species alignment tool (CAT)".BMC BIOINFORMATICS 8.1(2007):-.
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