The MEME Suite

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

The ceqlogo program generates one or multiple, aligned logos in EPS or PNG format, based on a set of 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 PNG 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)

Motif File

A file containing one or more motifs in MEME format.

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

Option	Parameter	Description	Default Behavior
Options with arguments
-i	motif file	Load all motifs within the motif file.
-m	id or num	Load the numth motif or the motif whose ID is id within the motif file specified by the previous -i option.
-ix	motif file	Load the xth motif or the motif whose ID is x within the motif file.
-r		Reverse-complement the logo for the previous -i or -m option.
-l		Load motifs by IDs, preferentially.	Load motifs in input order, preferentially.
-s	shift	Offset the previously loaded motif by shift.
-b	bar bits	Number of bits in bar (real # > 0).	DNA motifs have a default height of 2 bits and protein motifs have a default height of 4.3 bits.
-c	tic bits	Number of bits between tic marks.
-e	error bar fraction	Fraction of error bar to show (real # > 0).
-f	EPS|PNG	Set the format of the output.	The output is created in EPS.
-F		Create a frequency logo with stack height 1.	Height of stack is information content of motif column.
-h	logo height	Height of output logo in cm (real # > 0).
-o	image file	Create an image called image file and send the output to it.	Send the output to standard out.
-n	sample number	Set the sample count of the previously loaded motif to sample number. This value is used to calculate error bars.	Use the sample count embedded in the motif file.
-t	title label	Set the title of the image to title label.
-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	pseudocount	Pseudocount for motifs.	A pseudocount value of 1 is used.
-d	fineprint	Print fineprint in small font at bottom of logo.	"Ceqlogo " is printed.
--test	verbosity level	Runs a self test, ignoring all other options. The verbosity level [0..3] is optional.
Toggles
-S		Turn off small sample correction.	Small sample correction is used.
-B		Toggle bar ends.
-E		Toggle error bar.
-O		Toggle outlining of characters.
-N		Toggle numbering of x-axis.
-X		Toggle boxing of characters.
-Y		Toggle y-axis.