psp-gen -pos <primary sequence file> -neg <control sequence file> [options]
psp-gen is used to allow MEME to perform discriminative motif discovery—to find motifs overrepresented in one set of sequences compared to in another set. It takes two files as input—the sequence file to be input to MEME, (the "primary" file) and a "control" sequence file of sequences believed not to contain the same motifs as in the "primary" file. psp-gen creates a file for use by MEME that encapsulates information about probable discriminative motifs. psp-gen records its chosen motif width in the file, and MEME is able to adjust the data when it tries different motif widths.
The name of a file containing FASTA formatted sequences that are to be used as the primary set in PSP calculation.
The name of a file containing FASTA formatted sequences that are to be used as the control set in PSP calculation.
A FASTA-like PSP format is written to standard output, it contains a prior for every position of every sequence in the primary set.
Option | Parameter | Description | Default Behavior |
---|---|---|---|
General Options | |||
-minw | minw | The minimum width to use with selecting the "best" width for PSPs. | The minimum width is set to 4. |
-maxw | maxw | The maximum width to use with selecting the "best" width for PSPs. | The maximum width is set to 20. |
-triples | Use spaced triples instead of whole-word matches. Recommended for protein. | Whole-word matches are used. | |
-fixedstart | When using the -triples option, only consider triples starting at the start of the site. | Allow triples to start anywhere in a width w site. | |
-equiv | Letter Groups | Any sequence of letter that appears together should be matched as equal. Separate letter groups using "-", e.g. -equiv "IVL-HKR" means treat all occurrences of I, V or L as the same, and all occurrences of H, K or R as the same. Note that in alphabets where '-' is an allowed symbol separate groups may be specified by repeating the -equiv option for each group. | No letter groups are used. |
-revcomp | Both strands are considered when calculating PSPs for complementable alphabets. | Only the given strand is considered. | |
-scalemin | min score | The lowest score value after scaling. | The lowest score is set to 0.1, unless the -scalemax option is set in which case the lowest score is max score - 1. |
-scalemax | max score | The highest score value after scaling. | The highest score is set to 0.9, unless the -scalemin option is set in which case the highest score is min score + 1. |
-maxrange | Choose the width with the biggest difference between minimum and maximum scores (before scaling). | Choose the width with the biggest maximum score (before scaling). | |
-raw | Output scores instead of priors. | The program output PSPs. | |
-reportscores | Send to standard error primary and control file names, min and max scores and min and max widths, tab-separated. | Do not report scores to standard error. | |
-verbose | Send detailed stats to standard error, reporting frequency of each score. | No extra information is reported. |
In each example, the sequence file is the same as the positive set used
for psp-gen
. While there is no check that you have done
this because MEME runs as a separate program (other than that the
sequence names need to match, as do the number of sites), using a
primary set different to the sequence set MEME searches is unlikely
to be useful.
Generate a discriminative prior for a DNA sequence set
(pos-dna.fasta
) likely to contain TF binding sites, given
another DNA sequence set unlikely to contain TF binding sites
(neg-dna.fasta
):
psp-gen -pos pos-dna.fasta -neg neg-dna.fasta > dna.psp
Use these position-specific priors in MEME, searching both strands:
meme pos-dna.fasta -psp dna.psp -oc meme_out_dna
-revcomp
Generate a discriminative prior for a protein sequence set
(pos-prot.fasta
) associated with a specific function, given
another protein sequence set unlikely to relate to that function
(neg-prot.fasta
):
psp-gen -pos pos-prot.fasta -neg neg-prot.fasta -protein
-triples -maxrange > prot.psp
Use these position-specific priors in MEME:
meme pos-prot.fasta -psp prot.psp -oc meme_out_prot
View usage information:
psp-gen -h
The psp-gen program generates a position-specific
prior (PSP) in a data file, which can be used as an additional input
to MEME to bias the search to sites more likely to
contain a motif (or motifs) of interest. Without using a PSP, MEME
assigns the same prior probability to all sites. A PSP is generated
by psp-gen
using two sequence sets, each
in FASTA format:
The basic principle of a discriminative prior is to start from the question:
What fraction of all instances of a w-wide subsequence (or w-mer) across both sequence sets occur in the primary set?
The intuition is that any w-mer that is common in the primary set but not the control set could form part of motif of interest, based on the way the two sets are chosen.
PSP calculation starts from the following equation based on the
D-prior described in the Narlikar et al. RECOMB
2007 paper
"Nucleosome
Occupancy Information Improves de novo Motif
Discovery". We count the number of instances
Xi,j(w) of the
subsequence w wide starting at position j in sequence
Xi of the primary set, and similarly
count Yi,j(w) in the control
set, then calculate for each site
As pseudocounts, we add 1 to the enumerator, and 1 +
|X|/|Y| to the denominator. The purpose of the
pseudocounts is to avoid giving a high score to infrequent
subsequences that are not (or rarely) found in the control set. Once
we have scored all sites for a given value of w
, we scale
scores to a range that can be set on the command
line, with the default range [0.1,0.9]
.
We repeat scoring for the whole range of motif widths under
consideration, and choose a "best" width using one of two methods:
either we choose the value of w
that maximizes the score
over all sequences, or the value of w
that maximizes the
difference between the maximum and minimum score over all
sequences. We also allow an option of using spaced triples
instead of whole words to match
subsequences. See Variations below for more
details on triples and choosing the "best" width.
Once we have scored every available site and chosen a specific value
of w
, we convert the scores to probabilities, based on the
proportionalities
where Zi = j means
that the site for a motif in sequence Xi is found at
location j (with j = 0
signifying there is no site in the given sequence),
and Di,j is the score for
sequence Xi at the site starting at
location j, numbered from 1.
We convert these proportionalities to a PSP by normalizing them to add
up to 1 over each sequence.
Since MEME runs as a separate program, there is no way to check that the primary set is the same as the sequence set given to MEME. There are however checks that every name in the PSP file matches a name in the MEME sequence set, and that the number of sites in the PSP file for a particular sequence name matches the number of sites in the sequence file seen by MEME. While it does not make sense to use a completely different sequence set for PSP generation and for running MEME (with the resulting PSP file), MEME can use a PSP file that does not provide probabilities for every sequence. Any sequences not in the PSP file are given a uniform prior probability. MEME documentation includes more detail on how PSPs are used.
For each variation, "default" means that you do not need to specify a command-line switch to turn on that setting.
-revcomp
(the default is to score only the given
strand). This setting applies to both the primary and control
sequences.
-maxw
and -minw
provides limits to psp-gen
but
the algorithm chooses one width to generate priors after scoring the
range of allowed widths, using one of two variations:
-maxrange
):
choose the value of w that maximizes the difference between
the highest and lowest score over all sequences. This variant is
useful in data sets where a high number of sites achieve similar
high scores (more likely to happen with protein sequences).
-triples
): for a case
where exact-word matches are unlikely to succeed, spaced triples
are an alternative. Each w-wide word is broken down into
triples containing an initial, middle and final letter, and all
other letters are treated as don't cares (i.e., they match
anything). In spaced triples mode, psp-gen
scores a
site on the basis of the spaced triple fitting the w-wide
word at that site that has the highest score. For example, the
subsequenceMTFEKI
contains the following
triples:MT...I
M.F..I
M..E.I
M...KI
-fixedstart
, which only allows triples for the
current site under consideration that start at the beginning of the
site. This option reduces execution time at the expense of
considering fewer possibilities for scoring a site.
-scalemin
and
-scalemax
): the scoring formula creates values in the
range [0,1]
, but the conversion to PSPs from scores
requires values strictly less than 1. Choosing an option other than
scaling between the default [0.1,0.9]
reduces (if you
narrow the range) or increases (if you widen the range) sensitivity
to small differences in scores. If you only set one
of scalemin
or scalemax
, the other is
calculated as described in Options.
-equiv
option to treat specific groups of letters
as if they were all the same (default: all letters are treated as
unique). For more detail, see Options.
-raw
stops the last stage
of computation that converts the scores to probabilities; the
scores sent to standard out are however scaled, using either the
defaults or selected values of scalemin
and scalemax
(default: convert scores to PSPs).
-reportscores
in Options
(default: do not report).
-verbose
causes
detailed statistics on scores to be sent to standard error
(default: no statistics reported).
The running time of psp-gen scales linearly in the sizes of the positive and negative sequence sets (X and Y), and faster than linearly in the difference between the maximum and minimum motif widths (N = maxw-minw). Running time using the default method (exact word match) is O((|X| + |Y|)(Nlog(N))). Running time using the spaced triples method (option -triples) is approximately O((|X| + |Y|)(Nlog2(N))).
The plots below show actual running times of psp-gen on a 4 GHz Intel Core i7 processor with 16GB of memory on inputs containing different numbers of sequences in the positive and negative sets, and specifying different values of the maximum motif width (option -maxw), and different methods—exact word match (default) or spaced triples (option -triples)