PAC: Progressive Alignment with Consensus Sequences

is one of the major open problems in computational molecular biology. The purpose of this study was to provide a new method, PAC (Progressive Alignment with Consensus Sequences), for calculation of multiple amino acid sequence alignments. In PAC, multiple alignments are built by the successive application of pairwise alignment algorithms; the distance between two groups is defined as the distance between the two corresponding consensus sequences; group to group alignment is also calculated using the alignment of the consensus sequences. One advantage of PAC is that it is simple and efficient, and in many cases generates reasonable results. Another advantage of this method is that the scoring can be done with reference to the evolutionary tree, even though the tree structure itself may remain unknown.

[1]  O. Gotoh.  An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[2]  R. Schulz,et al.  Protein Structure Prediction , 2020, Methods in Molecular Biology.

[3]  T. Smith,et al.  Optimal sequence alignments. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Sandeep K. Gupta,et al.  Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment , 1995, J. Comput. Biol..

[5]  S. Altschul,et al.  A tool for multiple sequence alignment. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R F Doolittle,et al.  Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. , 1996, Methods in enzymology.

[7]  M. Sternberg.  Protein Structure Prediction: A Practical Approach , 1997 .

[8]  J. Lakey,et al.  The bacterial porin superfamily: sequence alignment and structure prediction , 1991, Molecular microbiology.

[9]  U. Melcher,et al.  The '30K' superfamily of viral movement proteins. , 2000, The Journal of general virology.

[10]  D. Lipman,et al.  The multiple sequence alignment problem in biology , 1988 .

[11]  Dennis W. Ross,et al.  Molecular Biology of Cells , 1998 .

[12]  J. Richardson,et al.  Simultaneous comparison of three protein sequences. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. O. Dayhoff,et al.  22 A Model of Evolutionary Change in Proteins , 1978 .

[14]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[15]  Susan R. Wilson.  INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .

[16]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[17]  R. Doolittle,et al.  Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.

[18]  W R Taylor,et al.  Hierarchical method to align large numbers of biological sequences. , 1990, Methods in enzymology.

[19]  Edsger W. Dijkstra,et al.  A note on two problems in connexion with graphs , 1959, Numerische Mathematik.

[20]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .

[21]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[22]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Dan Gusfield,et al.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .