In communication systems information is conveyed from the transmitter side to the receiver side. The delivered information passes through a generally noisy communication medium. An example of noise is when the transmitted symbols are substituted or deleted and irrelevant symbols are inserted. Thence, the received signal is corrupted and a processing state is needed to recover the disturbances. This thesis presents a unique error correction method for substitutions, insertions and deletions in a quaternary alphabet. The fundamentals are based on watermark coding that is a technique presented by Davey and MacKay according to the forward-backward algorithm which deals only with binary errors. This work discusses firstly the common schemes for error correction in communication systems with binary symmetric channels. However, a generalization of the recovery strategy is needed in biological applications as well as quaternary communication channels. Through the thesis, a generalized recovery scheme is proposed which allows an error correction within a quaternary alphabet that is required in a DNA sequencing process. A platform for correcting the lost frame synchronization is provided as a marker code. Moreover, a better performance is achieved by using an algebraic code in concatenation with the watermark code. The explained techniques are implemented and investigated for a range of different design parameters and scenarios.