Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
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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.
Key wordsMultiple sequence alignments Evolutionary trees
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- Dayhoff MO, Eck RV (1968) Atlas of protein sequence and structure 1967–1968, National Biomedical Research Foundation, Silver Spring MD, p 19Google Scholar
- Dayhoff MO, Park CM, McLaughlin PJ (1972) Building a phylogenetic tree: cytochrome c. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5. National Biomedical Research Foundation, Washington DC, pp 7–16Google Scholar
- Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model for evolutionary change. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington DC, pp 345–358Google Scholar
- Fredman ML (1984) Computing evolutionary similarity measures with length independent gap penalties. Bull Math Biol 46:553–566Google Scholar
- Hunt LT, Hurst-Calderone S, Dayhoff MO (1978) Globins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. National Biomedical Research Foundation, Washington DC, pp 229–249Google Scholar
- Kernighan BW, Ritchie DM (1978) The C programming language. Prentice-Hall, Englewood Cliffs NJGoogle Scholar
- Steffens GJ, Bannister JV, Bannister WH, Flohe L, Gunzler WA, Kim S-MA, Otting F (1983) The primary structure of Cu-Zn superoxide dismutase fromPhotobacterium leiognathi: evidence for a separate evolution of Cu-Zn superoxide dismutase in bacteria. Hoppe-Seyler's Z Physiol Chem 364:675–690PubMedGoogle Scholar