/usr/share/doc/glam2/alphabet.html is in glam2 1064-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html lang=en>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>GLAM2 Alphabets</title>
<link type="text/css" rel="stylesheet" href="glam2.css">
</head>
<body>
<h1>GLAM2 Alphabets</h1>
<h2>Alphabet files</h2>
<p>Alphabet files allow glam2 and glam2scan to operate on sequences
over arbitrary, user-defined alphabets. They also allow residue
abundances to be specified. Their format is inspired by that of <a
href="http://www.vmatch.de/">vmatch</a>. For examples, see
robinson.alph and dna.alph in the GLAM2 examples directory.</p>
<p><strong style="color: red">Note:</strong> as soon as you specify an
alphabet file, the glam2 programs lose all knowledge about residues'
tendencies to align with each other. So, if you use an alphabet file
to specify amino-acid or nucleotide abundances, you probably want to
specify a <a href="dirichlet.html">Dirichlet mixture</a> file too:
recode3.20comp or glam_tfbs.1comp.</p>
<p>In alphabet files, the # character introduces a comment: everything
from it to the end of the line is ignored. Otherwise, each non-blank
line defines a symbol of the alphabet. The first non-whitespace
character on the line is the main character representing the symbol:
this is how the symbol is printed. Any characters that follow it
without any whitespace are aliases (when reading input). This is
optionally followed by whitespace and then a number, indicating the
abundance of the symbol. The abundances can be counts, fractions, or
percentages: they will be normalized so that they sum to 1.
Unspecified abundances default to 1. The final symbol is the
<em>wildcard</em>: it is forbidden from appearing in aligned columns,
and all characters not defined in the alphabet file are aliases of it.
No abundance is defined for the wildcard (any number will be
ignored).</p>
<p>The order of the symbols matters when reading Dirichlet mixture
files or looking at reverse strands.</p>
<h2>Built-in alphabets</h2>
<p>The p (protein) alphabet is equivalent to using robinson.alph (and
recode3.20comp) in the GLAM2 examples directory. The n (nucleotide)
alphabet is equivalent to using dna.alph (and glam_tfbs.1comp) in the
GLAM2 examples directory.</p>
<h2>FASTA format</h2>
<p>When reading sequences in FASTA format, the > character begins
the title of the next sequence, which continues till the end of the
line. In the sequence itself, whitespace is always ignored, and
non-whitespace characters are always part of the sequence: if not
defined in the alphabet file, they are interpreted as wildcards.</p>
<h2>Reverse strands</h2>
<p>glam2 and glam2scan provide options to look at both strands of the
input sequences. This may only be meaningful for nucleotide sequences,
but is actually defined for all alphabets. The reverse strand is
obtained by first reversing the sequence, and then swapping each
symbol with its opposite in the alphabet's order (apart from
wildcards). Thus, for nucleotides, these symbols are swapped: a:t and
c:g. For proteins, these symbols are swapped: A:Y, C:W, D:V, E:T, F:S,
G:R, H:Q, I:P, K:N, and L:M.</p>
</body>
</html>
|