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  • 1
    Electronic Resource
    Electronic Resource
    Concurrent Neutral Evolution of mRNA Secondary Structures and Encoded Proteins (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 238-242 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Neutral evolution — mRNA secondary structures — Function conservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure. We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient search for new variants on the protein level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910027
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Neutral adaptation of the genetic code to double-strand coding (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 407-416 
    Details
    ISSN: 1432-1432
    Keywords: Genetic code ; Sense-antisense coding ; Neutral adaptation ; Information content
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We lay new foundations to the hypothesis that the genetic code is adapted to evolutionary retention of information in the antisense strands of natural DNA/RNA sequences. In particular, we show that the genetic code exhibits, beyond the neutral replacement patterns of amino acid substitutions, optimal properties by favoring simultaneous evolution of proteins encoded in DNA/RNA sense-antisense strands. This is borne out in the sense-antisense transformations of the codons of every amino acid which target amino acids physicochemically similar to each other. Moreover, silent mutations in the sense strand generate conservative ones in its antisense counterpart and vice versa. Coevolution of proteins coded by complementary strands is shown to be a definite possibility, a result which does not depend on any physical interaction between the coevolving proteins. Likewise, the degree to which the present genetic code is dedicated to evolutionary sense-antisense tolerance is demonstrated by comparison with many randomized codes. Double-strand coding is quantified from an information-theoretical point of view.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02406718
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 691-698 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Evolutionary models — Correlated sequence sites — Secondary structure — Alignment — Rate heterogeneity — Phylogenetic analysis — Maximum-likelihood inference — Monte Carlo simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition–transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006590
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    A local algorithm for DNA sequence alignment with inversions (1992)
    Springer
    Bulletin of mathematical biology 54 (1992), S. 521-536 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A dynamic programming algorithm to find all optimal alignments of DNA subsequences is described. The alignments use not only substitutions, insertions and deletions of nucleotides but also inversions (reversed complements) of substrings of the sequences. The inversion alignments themselves contain substitutions, insertions and deletions of nucleotides. We study the problem of alignment with non-intersecting inversions. To provide a computationally efficient algorithm we restrict candidate inversions to theK highest scoring inversions. An algorithm to find theJ best non-intersecting alignments with inversions is also described. The new algorithm is applied to the regions of mitochondrial DNA ofDrosophila yakuba and mouse coding for URF6 and cytochrome b and the inversion of the URF6 gene is found. The open problem of intersecting inversions is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02459633
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    Paper (German National Licenses)
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