Illustration of some of the formatting capabilities of ALSCRIPT.
(a) A small AMPS block file. Each aligned sequence is represented by a column. This block file includes character-based histograms that show the result of a combined secondary structure prediction method [Russell et al., 1992]. (b) An ALSCRIPT command file. Comment lines start with a #character, sections A-C set up general layout definitions: the ADD_SEQcommand allows extra space to be inserted in the alignment at any location, 39 3 means add space for three sequences after sequence 39. PORTRAIT specifies that the output will be arranged with the longest side of the paper vertical. POINTSIZE sets the default pointsize for plotting characters. The DEFINE_FONTcommands set up the fonts that are to be used and their pointsize; font 0 is used as the default. The pointsize may be set to the default value, an explicit value, or relative (REL) to the default size. Sections D-E show the boxing, shading and font changing commands in action. The IDENT_FONTALL 6 specifies font 6 (Times-Roman) for all identifiers. SURROUND_CHARSLIV ALL specifies that all L I and V characters will be separated from other characters by a line (e.g. at sequence positions 19-21). FONT_CHARSKR ALL 4 switches the font of K and R characters to font 4 (Times-Bold 10 point). When regions are selected the coordinates are given in character units with the origin at the top left hand corner of the plotted alignment. For example, BOX_REGION14 1 16 38 means box from residue 14 to 16 of sequences 1 to 38. These coordinates apply irrespective of how many pages are needed to plot the alignment at the chosen pointsize. The SHADE_CHARScommand permits specific characters to be shaded with a grey value; The INVERSE_CHARScommand allows white lettering to be superimposed on the shaded background, as shown for D and E. LINE TOP 2 40 8 draws a horizontal line at the top of the characters from residue 2 to 8 of sequence 40, similar commands allow lines at the left, right and below the defined residues; SUB_IDchanges the identifier code for a sequence and SUB_CHARSallows a character to be substituted with another. In the example shown here, SUB_CHARSis used to remove the H, E and T characters that made up the prediction histograms and replace them with SPACE ` 'characters. The similar commands used to format the Sheet, Turn and Summary predictions are ommited for brevity.