Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling |
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| Authors: | Smith Randall F; Smmith Temple F |
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| Affiliation: | Molecular Biology Computer Research Resource. Department of Biostatistics, Dana-Farber Cancer Institute and School of Public Health, Harvard University 44 Binney St., Boston, MA 02115, USA |
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| Abstract: | A multiple sequence alignment algorithm is described that usesa dynamic programming-based pattern construction method to aligna set of homologous sequences based on their common patternof conserved sequence elements. This pattern-induced multi-sequencealignment (PUMA) algorithm can employ secondary-structure dependentgap penalties for use in comparative modelling of new sequenceswhen the three-dimensional structure of one or more membersof the same family is known. We show that the use of secondarystructure information can significantly improve the accuracyof aligning structure boundaries in a set of homologous sequenceseven when the structure of only one member of the family isknown |
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| Keywords: | alignments/ homology/ modelling/ protein sequence/ secondary structure |
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