ALSCRIPT takes a multiple sequence alignment in AMPS (Barton &Sternberg, 1987, Barton, 1990) block-file format and a set of formatting commands and produces a PostScript file that may be printed on a PostScript laser printer, or viewed using a PostScript previewer (e.g. Sun Microsystem's PageView program). CLUSTAL and GCG format multiple alignment files may also be used (see below). ALSCRIPT is NOT a multiple sequence alignment program, nor is it an alignment editor.
Given a block-file and pointsize (character width/height), ALSCRIPT calculates how many residues can be fitted across the page, and how many sequences will fit down the page, it then prints the alignment at the chosen pointsize on as many pages as are needed. Running ALSCRIPT with a smaller or larger pointsize will automatically re-scale the alignment to fit on fewer or more pages as appropriate. The actual page dimensions may be re-set to any value, so if you have access to an A3 PostScript printer, or typesetting machine, alignments can readily be scaled to maximise the available space.
Each output page has three basic regions. The left hand edge contains identifier codes for each sequence. The main part of the page holds the alignment, and the top part, the position numbers and tick marks. ALSCRIPT commands make use of a character coordinate system for font changes, and other formatting commands. Thus, any residue in the alignment may be referred to by its sequence position number (x-axis) and sequence number (y-axis), similarly, ranges of residue positions, or sequences may also be defined in the character coordinate system.
The basic ALSCRIPT commands allow the following functionality:
Fonts: Any PostScript font at any size may be defined and used on individual residues, regions or identifier codes.
Boxing: Simple rectangular boxes may be drawn around any part of the alignment. Particular residue types may be selected and automatically "surrounded" by lines. For example, if the characters 'G' and 'P' are selected, then lines will not be drawn between G and P characters, but only where G and P border with other characters.
Shading: Grey shading of any level from black to white may be applied to any region of the alignment, either as a rectangular region, or as residue specific shading. e.g. "shade all Cys residues between positions 6 and 30"
Text: Specific text strings may be added to the alignment at any position and in any font or font size.
Lines: Horizontal or vertical lines may be drawn to the left, right, top or bottom of any residue position or group of positions.
Colour: Characters or character backgrounds may be independently coloured.
The example block file "example1.blc" and command file "example1.als" illustrate most of these commands in action.
Although written with the aim of producing figures for journal submission, ALSCRIPT may be used as a tool for interpreting multiple sequence alignments. For example, the boxing, shading and font changing facilities can be applied to highlight amino acids of a particular type and thus draw attention to clusters of positive or negative charge, hydrophobics, etc.