Progressive sequence alignment as a prerequisitetto correct phylogenetic trees View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1987-08

AUTHORS

Da-Fei Feng, Russell F. Doolittle

ABSTRACT

A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: "once a gap, always a gap." The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods. More... »

PAGES

351-360

References to SciGraph publications

  • 1985-02. Aligning amino acid sequences: Comparison of commonly used methods in JOURNAL OF MOLECULAR EVOLUTION
  • 1984-07. Algorithms for computing evolutionary similarity measures with length independent gap penalties in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1982-11. Accuracy of estimated phylogenetic trees from molecular data in JOURNAL OF MOLECULAR EVOLUTION
  • 1979-07. The complete amino acid sequence of copper, zinc superoxide dismutase from Saccharomyces cerevisiae in CARLSBERG RESEARCH COMMUNICATIONS
  • 1981-01. The old REH theory remains unsatisfactory and the new REH theory is problematical - a reply to holmquist and jukes in JOURNAL OF MOLECULAR EVOLUTION
  • 1981-01. The current status of REH theory in JOURNAL OF MOLECULAR EVOLUTION
  • 1986-07. Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla in NATURE
  • 1984-06. The alignment of sets of sequences and the construction of phyletic trees: An integrated method in JOURNAL OF MOLECULAR EVOLUTION
  • 1980-06. Sequence homologies amongE. coli ribosomal proteins: Evidence for evolutionarily related groupings and internal duplications in JOURNAL OF MOLECULAR EVOLUTION
  • 1986-09. A method for the simultaneous alignment of three or more amino acid sequences in JOURNAL OF MOLECULAR EVOLUTION
  • 1974-03. The phylogeny of human globin genes investigated by the maximum parsimony method in JOURNAL OF MOLECULAR EVOLUTION
  • 1986-09. Copper/Zinc superoxide dismutase: How likely is gene transfer from ponyfish toPhotobacterium leiognathi? in JOURNAL OF MOLECULAR EVOLUTION
  • Journal

    TITLE

    Journal of Molecular Evolution

    ISSUE

    4

    VOLUME

    25

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/bf02603120

    DOI

    http://dx.doi.org/10.1007/bf02603120

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1022962956

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/3118049


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    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/bf02603120'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/bf02603120'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf02603120'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf02603120'


     

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