Title :
A Fast Algorithm for Detecting Frame Shifts in DNA sequences
Author :
Masoom, Hassan ; Datta, Suprakash ; Asif, Amir ; Cunningham, Lesley ; Wu, Gillian
Author_Institution :
Dept. of Comput. Sci. & Eng., York Univ., Toronto, Ont.
Abstract :
Sequencing technologies used to generate long strands of DNA are susceptible to laboratory errors that may result in several DNA nucleotides being deleted from the genome. Detecting such deletions in the protein coding regions is of utmost importance. Missing even a single nucleotide may lead to frame shifts with all the following codons (and consequently the encoded amino acids) being identified incorrectly. In addition to the deletion of nucleotides during sequencing, frame shifts can occur because of a variety of other reasons including mutations. In this paper, we present a fast computational technique to identify frame shifts in protein coding regions in DNA sequences. Our technique is based on Fourier spectral characteristics of coding regions in DNA sequences. We provide two applications of our technique - detecting deletions in DNA sequences in coding regions and also detecting frame shifts in viral DNA
Keywords :
DNA; Fourier analysis; biology computing; encoding; molecular biophysics; proteins; sequences; spectral analysis; DNA nucleotides; DNA sequences; Fourier spectral characteristics; frame shift detection; nucleotides deletion; protein coding region; Bioinformatics; Biology computing; DNA; Genomics; Humans; Laboratories; Machine learning algorithms; Organisms; Proteins; Sequences;
Conference_Titel :
Computational Intelligence and Bioinformatics and Computational Biology, 2006. CIBCB '06. 2006 IEEE Symposium on
Conference_Location :
Toronto, Ont.
Print_ISBN :
1-4244-0623-4
Electronic_ISBN :
1-4244-0624-2
DOI :
10.1109/CIBCB.2006.330971
