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Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices,10.1093/bioinformatics/18.8.1102,Bioinformatics/co

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices   (Citations: 15)
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Motivation: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring. Results: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive anal- ysis of the possible simplified amino acid alphabets, us- ing a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the sim- plified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the per- formance becomes worse, taking up to several hours, for highly simplified alphabets. Availability: AlphaSimp and other accessory pro- grams are available at http://bioinformatics.cribi.unipd.it/
Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 18, no. 8, pp. 1102-1108, 2002
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    • ...Our conclusion is further supported by the fact that grouping amino acid residues into five sets is most common in the literature (Dayhoff et al., 1972; Li et al., 1997, 2003; Wolynes, 1997; Murphy et al., 2000; Wang and Wang, 2002, 1999; Cieplak et al., 2001; Cannata et al., 2002; Koisol et al., 2004)...

    Sourav Rakshitet al. An amino acid map of inter-residue contact energies using metric multi...

    • ...Grouping twenty amino acids into a smaller alphabet is shown to be useful [3]...
    • ...By making use of the relationship among amino acids, it is expected that detection of patterns in sequence alignments may be achieved in a simpler manner [3]...
    • ...It is also expected that the proposed grouping may be useful in modeling and in protein design, and in finding consensus sequences [3][4][8] in bioinformatics approaches...

    B. G. Kim. Complementary grouping of amino acids based on base-pairing

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