A Template-Based Mixed-Integer Linear Programming Sequence Alignment Model

The similarity of DNA or protein sequences between species is an approximate measure of the evolutionary distance between them. By identifying and aligning pairs of sequences, knowledge of the genetic importance of a gene or protein of one species can be extended to a second, relatively unknown species with a similar sequence.

[1]  C. Floudas.  Nonlinear and Mixed-Integer Optimization: Fundamentals and Applications , 1995 .

[2]  K. Palczewski,et al.  Crystal Structure of Rhodopsin: A G‐Protein‐Coupled Receptor , 2002, Chembiochem : a European journal of chemical biology.

[3]  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.

[4]  C. D. Livingstone,et al.  Molecular modelling of D2-like dopamine receptors. , 1992, The Biochemical journal.

[5]  J. Deisenhofer,et al.  Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution , 1975 .

[6]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[7]  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.

[8]  Olivier Poch,et al.  A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..

[9]  D. Sibley,et al.  D2-like Dopamine Receptors , 2008 .

[10]  T. Branchek,et al.  Modeling the G-protein-coupled neuropeptide Y Y1 receptor agonist and antagonist binding sites. , 1997, Protein engineering.

[11]  W. C. Probst,et al.  Sequence alignment of the G-protein coupled receptor superfamily. , 1992, DNA and cell biology.

[12]  Robert Huber,et al.  Structure of bovine pancreatic trypsin inhibitor , 1984 .

[13]  M. Waterman,et al.  A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. , 1987, Journal of molecular biology.

[14]  Kun-Mao Chao,et al.  A generalized global alignment algorithm , 2003, Bioinform..