Pair-wise alignment of protein sequences and local similarity searches produce many false positives because of compositionally biased regions, also called low-complexity regions (LCRs), of amino acid residues. Masking and filtering such regions significantly improves the reliability of homology searches and, consequently, functional predictions. Most of the available algorithms are based on a statistical approach. We wished to investigate the structural properties of LCRs in biological sequences and develop an algorithm for filtering them.