HELP! -Check Engine Light

Hi, I have a 1989 325i. Its in excellent condition with little to no damage with 70,000 miles. Last week, I accidentally left my light on and my battery was dead. In attempt to help me my brother tried to jump the battery. But failed terribly by accidentally putting the positive on the negative, and negative wire on the positive. There were sparks but we quickly realized our mistake and corrected it. Everything seems fine now except my stereo won't work and my check light continuously flashes, and a red light over the check engine stays on. Everything seems fine so does anyone know what maybe wrong?