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

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  • 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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