Index
 Introduction
 Running ELPH
 Running the program as a motif finder
 Algorithm overview
 Command line options
 Running the program to compare the significant difference of a motif appearances in two different files
 Obtaining ELPH
I. Introduction
ELPH is a generalpurpose Gibbs sampler for finding motifs in a
set of DNA or protein sequences. The program takes as input a set
containing anywhere from a few dozen to thousands of sequences,
and searches through them for the most common motif, assuming that
each sequence contains one copy of the motif. We have used ELPH
to find patterns such as ribosome binding sites (RBSs) and exon
splicing enhancers (ESEs).
II. Running ELPH
There are two different ways to run the program: as a motif finder, or
as a tool to measure if there is any significant difference between the
appearances of a motif in two different files.
II.1 Running the program as a motif finder
In this case the input of ELPH is a file in multi FASTA format
containing the sequences:
elph <multifasta_file> [options]
Common usage:
elph DNAseqs.fasta LEN=5
II.1.1 Algorithm overview
The common usage of the program is to use as motif finder a Gibbs
site sampler. The programs begins by randomly selecting one motif
element in each sequence. After this initially setup the program
iteratively runs through the following two steps:
 predictive update step: one sequence from the input file is selected,
beginning with the first sequence and proceeding to the last
sequence. The current motif element from the sequence is added too
the background and the motif matrix is updated accordingly.
 sampling step: each possible starting position for a motif in the
given sequence is assigned a probability of being a motif starting at
that position; after that, a motif element is assigned to the sequence
by performing a weighted sample from all the possible positions.
These steps are repeated until a local maximum is reached or a fixed
maximum number of iterations are made. The Gibbs sampler is restarted
several times with a different seed in order to avoid trappings into a
local maximum. Once the motif alignment is found, the posteriori value
of the alignment is computed. An optimizing procedure is run to
maximize this posteriori value returning the MAP (maximum a posteriori
probability) of the motif.
II.1.2 Command line options
Several command line options can be specified:
 LEN=n : n is the length of the searched motif; if the length of the
motif is not given, the program will ask for it from stdin.
 ITERNO=n : n represents the maximum number of times that the Gibbs
sampler is restarted in order to avoid trapping into the local
maximum; default=10.
 MAXLOOP=n : n represents the maximum number of iterations used by the
program to compute the local maximum; default = 500.
 SGFNO=n : n is the number of iterations to compute significance of
motif (see also the g option); default = 1000.
 h : prints a help with the options the program.
 o <out_file> : write output in <out_file> instead of stdout
 a : by default the multiFASTA file is considered to contain DNA
sequences; if this option is specified the input file would be
considered to contain amino acid sequences (this option has not
been tested yet!).
 s <seed> : sets the seed for the random generation.
 p n : n represents the number of iterations before deciding that
the local maximum has been reached; default=20.
 b : if this options is specified then only matrix frequencies for
the background and the motif are printed; i.e. the positions of
each motif element within the sequence are not shown.
 x : normally the output of the program shows the motif elements that
contributed to the computation of the motif matrix; if the x
option is used the output will also show for each sequence those
positions which give the maximal score by using the computed
motif matrix (can be different from the motif elements'
positions).
 m <motif> : use the given pattern <motif> to compute its best fit
matrix to the data.
 g : if this option is specified then a significance of the motif
found is computed by comparing the appearances of the motif
elements within the input file to the appearances of the motif
within a randomly generated file containing sequences of the
same lengths as in the input file and with the same residue
distribution. The randomly generated file is paired to the
input file. Given the motif matrix, motif sampling is performed
a number of times (specified by SGFNO), and a probability of
occurrence of each motif element is computed in the two paired
samples. Two significance tests are used: the Wilcoxon pair test
(most reliable) and the student test.
 d : this option regards the way the significance of the motif is
computed; when v is specified, the probability of occurrence
of each motif element is estimated from the motif matrix, so
no there isn't necessary to run the Gibbs sampler SGFNO times;
this option should accompany the g option.
 v : if this option is given then the Gibbs sampler is not used
anymore, and the motif is computed in a deterministic way which
maximizes the MAP (faster).
 e : only when an additional file is used to test the significance
of the motif: find only the motifs that exactly match the
input pattern (m or t options)
 n [0..5] : degree of Markov chain used to generate the random file
used to test the significance of the motif
default = 2
 l : if the m option is specified too, computes the Least Likely
Consensus (LLC) score for the given motif; this score measure
the information content of the motif combined in respect to its
background rareness.
II.2 Running the program to compare the significant difference of a motif appearances in two different files
The input to ELPH in this case consists of two files in multi FASTA format:
elph <multifasta_file1> <multifasta_file2> [options]
The program computes a motif in <multifasta_file1 >
and then estimates if the motif is significantly more represented
in <multifasta_file1> compared to <multifasta_file2>. All the
options for computing the motif can be specified. There is an
additional option which can only be given to this way of running
the program:
t <matrix> : test if there is significant difference between the two
input files for a given motif matrix; <matrix> is the file
containing the motif matrix
III. Obtaining ELPH
ELPH is available free of charge under the opensource Artistic License.
To download ELPH please click here.
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