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In JoVE (1)
Other Publications (3)
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Articles by Benjamin Merget in JoVE
Benjamin Merget1,2, Christian Koetschan1, Thomas Hackl1, Frank Förster1, Thomas Dandekar1, Tobias Müller1, Jörg Schultz1, Matthias Wolf1
1Department of Bioinformatics, Biocenter, University of Würzburg, 2Institute of Pharmacy and Food Chemistry, University of Würzburg
ITS2 धन्यवाद वंशावली अनुमान एक साथ विचार अनुक्रम और आंतरिक लिखित 2 स्पेसर की माध्यमिक संरचना के लिए एक कार्यक्षेत्र है. यह सही एनोटेशन, संरचना भविष्यवाणी, एकाधिक अनुक्रम संरचना संरेखण और तेजी से पेड़ गणना के साथ डेटा संग्रह में शामिल हैं. संक्षेप में, इस कार्यक्षेत्र कुछ ही क्लिक करने के लिए पहली वंशावली विश्लेषण सरल है.
Other articles by Benjamin Merget on PubMed
BMC Research Notes. 2010 | Pubmed ID: 21108782
Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously.
PloS One. 2010 | Pubmed ID: 21209825
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.
Internal Transcribed Spacer 2 (nu ITS2 RRNA) Sequence-structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
PloS One. 2011 | Pubmed ID: 21347329
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.