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+<HEAD>
+<TITLE> Brief Description of ALSCRIPT</TITLE>
+</HEAD>
+<BODY><P>
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+<H1><A NAME=SECTION0007000000000000000> Brief Description of ALSCRIPT</A></H1>
+<P>
+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.
+<P>
+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.
+<P>
+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.
+<P>
+The basic ALSCRIPT commands allow the following functionality:
+<P>
+Fonts: Any PostScript font at any size may be defined and used on
+individual residues, regions or identifier codes.
+<P>
+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.
+<P>
+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"
+<P>
+Text: Specific text strings may be added to the alignment at any
+position and in any font or font size.
+<P>
+Lines: Horizontal or vertical lines may be drawn to the left, right, top
+or bottom of any residue position or group of positions.
+<P>
+Colour: Characters or character backgrounds may be independently
+coloured.
+<P>
+The example block file "example1.blc" and command file "example1.als"
+illustrate most of these commands in action.
+<P>
+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.
+<P>
+<HR> <A NAME=tex2html155 HREF=section3_8.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html153 HREF=alscript.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html147 HREF=section3_6.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html157 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
+<B> Next:</B> <A NAME=tex2html156 HREF=section3_8.html> New Features in </A>
+<B>Up:</B> <A NAME=tex2html154 HREF=alscript.html>No Title</A>
+<B> Previous:</B> <A NAME=tex2html148 HREF=section3_6.html> Installing ALSCRIPT</A>
+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
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