Title :
ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties
Author :
Carroll, Hyrum ; Clement, Mark ; Snell, Quinn ; McClellan, David
Author_Institution :
CS Dept., Brigham Young Univ., Provo, UT, USA
Abstract :
We present a new algorithm, ChemAlign, that uses physicochemical properties and secondary structure elements to create biologically relevant multiple sequence alignments (MSAs). Additionally, we introduce the physicochemical property difference (PPD) score for the evaluation of MSAs. This score is the normalized difference of physicochemical property values between a calculated and a reference alignment. It takes a step beyond sequence similarity and measures characteristics of the amino acids to provide a more biologically relevant metric. ChemAlign is able to produce more biologically correct alignments and can help to identify potential drug docking sites.
Keywords :
biochemistry; bioinformatics; drugs; ChemAlign; amino acids; biologically relevant multiple sequence alignment; drug docking sites; physicochemical property difference score; secondary structure elements; Amino acids; Bioinformatics; Biology; Chemical elements; Databases; Drugs; Laboratories; Matrices; Proteins; USA Councils; Physicochemical Properties Difference score; multiple sequence alignment; physicochemical properties;
Conference_Titel :
Bioinformatics and Biomedicine, 2009. BIBM '09. IEEE International Conference on
Conference_Location :
Washington, DC
Print_ISBN :
978-0-7695-3885-3
DOI :
10.1109/BIBM.2009.75
