An iterative algorithm for correcting sequencing errors in DNA coding regions

Insertion and deletion (indel) sequencing errors in DNA coding regions disrupt DNA-to-protein translation frames, and hence make most frame-sensitive coding recognition approaches fail. This paper extends the authors' previous work on indel detection and "correction" algorithms, and presents a more effective algorithm for localizing indels that appear in DNA coding regions and "correcting" the located indels by inserting or deleting DNA bases. The algorithm localizes indels by discovering changes of the preferred translation frames within presumed coding regions, and then "corrects" them to restore a consistent translation frame within each coding region. An iterative strategy is exploited to repeatedly localize and "correct" indels until no more indels can be found. Test results have shown that this improved algorithm can detect and "correct" more indels while not worsening the rate of introduction of false indels when compared to the authors' previous work.