The seqsel format output by JEvTrace (Joachimiak and Cohen, UCSF) is quite simple. The file refers to an associated multiple sequence alignment file in MSF format, and can be read and interpreted by the Chimera extension MSF Viewer (see importing JEvTrace information). Each line indicates the position of the residue in the alignment (not necessarily the same as its sequence number) to be colored (actually position minus one), the number of the sequence in which it should be colored (0 means all sequences in the alignment), and the red, green, and blue components of the color, each on a scale from 0 to 255. Example:
337 0 0 0 255Columns are separated by spaces and do not need to be aligned. The first line indicates that the residues at the 338th position in the alignment in all of the sequences should be colored blue. The second line indicates that the residue at position 341 of the alignment in the first (top) sequence should be colored cyan. The third line indicates that the residue at position 339 of the alignment in the 9th sequence should be colored yellow.
340 1 0 255 255
338 9 255 255 0
The format accomodates any 24-bit digital color and allows any subset of residues in any subset of sequences to be highlighted. The residue/coloring information is ordered hierarchically, i.e., smallest to largest sequence ID, and within this grouping, smallest to largest sequence position, and within this grouping, smallest to largest color values. This formula for sorting entries makes the data easier to read. Importantly, only the positions to be colored are encoded, minimizing disk space usage and maximizing the speed at which the information can be read.