Overview of MotifScope. Input to MotifScope consists of a set of sequences. MotifScope first identifies motifs by evaluating the length of consecutive sequence stretches formed by each k-mer present in the sequences. It then iteratively annotates consecutive occurrences of k-mers as motifs and masks them in the sequences. Subsequently, single occurrences of identified motifs are annotated and masked. To visualize the motif composition, motifs are colored based on their sequence similarity to each other. The sequences are then clustered based on their motif composition. It also offers the option to perform multiple sequence alignment (MSA) based on motif compositions.
