| Fragrep： An Efficient Search Tool for Fragmented Patterns in Genomic Sequences |
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| 作者姓名： | Mosig A Sameith K Stadler P |
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| 作者单位： | [1]Department of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China [2]Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig D-04103, Germany [3]Institute for Theoretical Chemistry, University of Vienna, Vienna A-1090, Austria [4]The Santa Fe Institute, Santa Fe, NM 87501, USA [5]Max Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany |
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| 摘 要： | Many classes of non-coding RNAs （ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum） can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.
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| 关 键 词： | 破碎模型 染色体序列 生物研究 基因研究 |
Fragrep: an efficient search tool for fragmented patterns in genomic sequences |
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| Mosig A,Sameith K,Stadler P.Fragrep: an efficient search tool for fragmented patterns in genomic sequences[J].Genomics Proteomics & Bioinformatics,2006,4(1):56-60. |
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| Authors: | Mosig Axel Sameith Katrin Stadler Peter |
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| Institution: | Department of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. mosig@sibs.ac.cn |
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| Abstract: | Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well- conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detect- ing the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme. |
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| Keywords: | Fragrep non-coding RNA detection fragmented pattern Dictyostelium discoideum |
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