A method and system for eliminating/suppressing long transition runs over a communications channel is disclosed. The method may include providing modulation coding based on a multi-level finite state machine (ML-FSM) having a periodic structure, the periodic structure being defined by a predetermined number of time frames. The ML-FSM may include a plurality of penalty-free edges for connecting nodes in one time frame to nodes at the same level in a subsequent time frame and a plurality of penalty edges for connecting nodes in one time frame to nodes at an upper level in the subsequent time frame. The method may further include utilizing the ML-FSM based modulation coding to facilitate data transmission over the communications channel.