ceqlogo

Usage: ceqlogo -i <filename> [options]

Examples:

Load all motifs within a MEME motif file and write to logo.eps in EPS format:
ceqlogo -i meme.motifs -o logo.eps -f EPS

Load second motif from each of two files and shift the first one:
ceqlogo -i2 meme1.motifs -s 3 -i2 meme2.motifs -o logo.eps -f EPS

Run a self-test:
ceqlogo -test

Description:

The ceqlogo program generates one or multiple, aligned logos in EPS or SVG format, based on a set of nucleotide or amino acid frequency matrices provided in the MEME file format. The code of ceqlogo is based on the Perl code of weblogo but is written in C and supports SVG output. Note that the program strives to use command line options similar to those of weblogo.

The letter stacks are calculated by the following equations found in Schneider and Stephens paper "Sequence Logos: A New Way to Display Consensus Sequences" and adapted from the weblogo documentation. The height of a letter is calculated as:

height(b,l) = f(b,l) * R(l)

where f(b,l) is the frequency of base or amino acid b at position l. The stack height R(l) is the amount of information present at position l and can be quantified as follows:

R(l) for amino acids = log(20) - (H(l) + e(n))

R(l) for nucleic acids = 2 - (H(l) + e(n))

where log is taken base 2, H(l) is the uncertainty at position l, and e(n) is the error correction factor for small sample sizes n. H(l) is computed as follows:

H(l) = - (Sum f(b,l) * log[ f(b,l) ])

where again, log is taken base 2. f(b,l) is the frequency of base b at position l. The sum is taken over all amino acids or bases.

The error correction factor e(n) is approximated by:

e(n) = (s-1) / (2 * ln 2 * n)

Input:

• <input filename> - A file containing one or more motifs in MEME format.

Output:

• If no output file is specified ceqlogo writes to standard output.

Options:

Options with arguments (all lower case):

• -i <input filename> - Loads all motifs within the file.
• -i<n> <input filename> - Loads the n-th motif within the file.
• -s <shift> - Shift for previously loaded motif (-i).
• -b <bar bits> - Number of bits in bar (real # > 0).
• -c <tic bits> - Number of bits between tic marks.
• -e <error bar fraction> - Fraction of error bar to show (real # > 0).
• -f <format> - Format of output (EPS,SVG). Default is EPS.
• -h <logo height> - Height of output logo in cm (real # > 0).
• -k <kind of data> - AA for amino acid, NA for nucleic acid.
• -o <output file> - Output file path. Default is stdout.
• -n <sample number> - Number of samples for previously loaded motif (-i). Used to calculate error bars.
• -t <title label> - Label for title.
• -w <logo width> - Width of output logo in cm (real # > 0)
• -x <x-axis label> - Label for x-axis.
• -y <y-axis label> - Label for y-axis.
• -p <pseudo counts> - Pseudo counts for motifs. Default is 1.0.
• -test [<verbosity level>] - Runs a self-test. All other options are ingored then. The verbosity level [0..3] is optional.

Toggles (all upper case):

• -B - Toggle bar ends.
• -E - Toggle error bar.
• -O - Toggle outlining of characters.
• -P - Toggle fineprint.
• -N - Toggle numbering of x-axis.
• -X - Toggle boxing of characters.
• -Y - Toggle y-axis.

Known problems:

• SVG output is only partially implemented.

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Author: Stefan Maetschke (s.maetschke@imb.uq.edu.au)