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Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

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Genomics, Proteomics & Bioinformatics 2006年第1期4卷 56-60页

作者： axel mosig Katrin Sameith Peter Stadler Department of Combinatorics and Geometry CAS/MPG Partner Institute for Computational Biology Shang-hai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China Max Planck Institute for Mathematics in theSciences Leipzig D-04103 Germany. BioinformaticsGroup Department of Computer Science and Interdisciplinary Center for Bioinformatics University of LeipzigLeipzig D-04103 Germany Institute for Theoretical Chemistry University of Vienna Vienna A-1090 Aus-tria The Santa Fe Institute Santa Fe NM 87501 USA

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.

关键词： Fragrep non-coding RNA detection fragmented pattern Dictyostelium discoideum

U7 snRNAs:A Computational Survey

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Genomics, Proteomics & Bioinformatics 2007年第3期5卷 187-195页

作者： Manja Marz axel mosig Brbel M.R.Stadler Peter F.Stadler Bioinformatics Group Department of Computer ScienceUniversity of LeipzigLeipzig D-04107Germany Department of Combinatorics and Geometry CAS/MPG Partner Institute for Computational BiologyShang-hai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China Max Planck Institute for Mathematics in the SciencesLeipzig D-04103Germany Max Planck Institute for Mathematics in the Sciences Leipzig D-04103Germany Bioinformatics Group Department of Computer ScienceUniversity of LeipzigLeipzig D-04107Germany Interdisciplinary Center for Bioin-formaticsUniversity of LeipzigLeipzig D-04107Germany Fraunhofer Institute for Cell Therapy and Im-munologyLeipzig D-04103Germany Department of Theoretical ChemistryUniversity of ViennaVienna A-1090Austria Santa Fe InstituteSanta FeNM 87501USA.

U7 small nuclear RNA （snRNA） sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.

关键词： U7 snRNA non-coding RNA RNA secondary structure evolution

Commuting between Two Worlds

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Bulletin of the Chinese Academy of Sciences 2014年第2期28卷 126-127页

作者： LUO Yuan axel mosig Institute of Coal Chemistry in shanxi Ruhr University in Bochum

China is one of the fastest growing economies worldwide. Are science and research also in the fast lane? We talked with LUO Yuan, scientist at the Institute of Coal Chemistry in Shanxi, and axel mosig, Professor at Ru... 详细信息

关键词：中国科学院世界材料科学固体化学马普学会德国研究所普朗克