A motif is a sequence pattern occurring repeatedly in a group of related DNA or protein sequences,and is an important concept for describing the common structure and function shared by the members of a protein family.However,the motif can be quite complex and is often difficult to predict the pattern of amino acid sequence.To get the desired results of the short motifs (2-4 polypeptides) derived from various bioinformatics is still a difficult task.The pep_pattern.pl can be used to solve this problem and provide a convenient set of Perl script for working with biological sequence motif.A Perl script pep_pattern.pl was written for searching very similar amino acid sequence pattern or motif in a group of related protein sequences by matching all the possible amino acids fragments permutation and counting frequency and position of each motif matched in sequence.