Article ID: | iaor2000877 |
Country: | United States |
Volume: | 10 |
Issue: | 3 |
Start Page Number: | 219 |
End Page Number: | 225 |
Publication Date: | Jul 1994 |
Journal: | Computer Applications in the Biosciences |
Authors: | Huang X.Q. |
Keywords: | programming: dynamic |
We present a dynamic progamming algorithm for identifying regions of a DNA sequence that meet a user-specified compositional requirement. Applications of the algorithm include finding C + G-rich regions, locating TA + CG-deficient regions, identifying CpG islands, and finding regions rich in periodical three-base patterns. The algorithm has an advantage over the simple window method in that the algorithm shows the exact location of each identified region. The algorithm has been implemented as a pol table C program called LCP (Local Content Program). LCP is extremely efficient in computer time and memory; it instantly locates all regions of a long DNA sequence meeting a given requirement. The LCP program was used to analyze the rabbit alpha-like globin gene cluster sequence.