new Fourier transform approach for protein coding measure based on the format of the Z curve

• Published in: Bioinformatics (Oxford, England) Vol. 14; no. 8; pp. 685 - 690
• Main Authors: Yan, M, Lin, Z.S, Zhang, C.T
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 1998
• Subjects: Algorithms; amino acid sequences; Biological and medical sciences; chemistry; computer aided gene recognition; computer analysis; computer software; DNA; DNA - chemistry; DNA - genetics; Evaluation Studies as Topic; Fourier Analysis; Fundamental and applied biological sciences. Psychology; General aspects; genetic code; genetics; lengthen shuffle fourier transform algorithm; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Nucleic Acid Conformation; proteins; Proteins - genetics; sequence periodicity; Performance evaluation; Fourier transformation; Gene; Nucleotide sequence; Computerized processing; Software; Method; Algorithm; Protein; Recognition
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/14.8.685

MOTIVATION: At the core of most protein gene-finding algorithms are the coding measures used to make a decision on coding/non-coding. Of the protein coding measures, the Fourier measure is one of the most important. However, due to the limited length of the windows usually used, the accuracy of the measure is not satisfactory. This paper is devoted to improving the accuracy by lengthening the sequence to amplify the periodicity of 3 in the coding regions. RESULTS: A new algorithm is presented called the lengthen-shuffle Fourier transform algorithm. For the same window length, the percentage accuracy of the new algorithm is 6-7% higher than that of the ordinary Fourier transform algorithm. The resulting percentage accuracy (average of specificity and sensitivity) of the new measure is 84.9% for the window length 162 bp. AVAILABILITY: The program is available on request fromC.-T. Zhang. Contact: ctzhang@tju.edu.cn