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Introduction
ccSeek is a graphical user interface developed to facilitate the discovery of motifs in protein sequences by means of sequence alignment. Interactive editing, a key feature of ccSeek, is intuitive to use and is performed using both mouse click-and-drag and menus; several menu editing actions have keyboard shortcuts. Protein sequences can be moved up, down, right, or left or even deleted, and vertical alignment lines can be added as needed to aid in editing. In addition, regions can be shaded in different colors to assist in alignment. Input files must be in FASTA format, edited alignments can be saved in FASTA format, and image views can be printed or saved in several standard file formats. Multiple windows can be opened for multiple input files with each window displaying a different amino acid property. Default properties included are hydropathy, size, polarity, charge, and identity, each with default values and colors, but users can change values and colors f
