In this paper, we exploit the analogy between protein sequence alignment and image pair correspondence to design a bioinformatics-inspired framework for stereo matching based on dynamic programming. This approach also led to the creation of a meaningfulness graph, which helps to predict matching validity according to image overlap and pixel similarity. Finally, we propose an automatic procedure to estimate automatically all matching parameters. This work is evaluated qualitatively and quantitatively using a standard benchmarking dataset and by conducting stereo matching experiments between images captured at different resolutions. Results confirm the validity of the computer vision/bioinformatics analogy to develop a versatile and accurate low complexity stereo matching algorithm.