emast

 

Function

Motif detection

Description

EMBASSY MEME is a suite of application wrappers to the original meme v3.0.14 applications written by Timothy Bailey. meme v3.0.14 must be installed on the same system as EMBOSS and the location of the meme executables must be defined in your path for EMBASSY MEME to work.

Usage:
ememe [options] mfile outfile

The outfile parameter is new to EMBASSY MEME. The output is always written to .

MAST: Motif Alignment and Search Tool

MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs.

A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. Motifs are represented as position-dependent scoring matrices that describe the score of each possible letter at each position in the pattern. Individual motifs may not contain gaps. Patterns with variable-length gaps must be split into two or more separate motifs before being submitted as input to MAST.

MAST takes as input a file containing the descriptions of one or more motifs and searches a sequence database that you select for sequences that match the motifs. The motif file can be the output of the MEME motif discovery tool or any file in the appropriate format.

MAST outputs three things:

MAST works by calculating match scores for each sequence in the database compared with each of the motifs in the group of motifs you provide. For each sequence, the match scores are converted into various types of p-values and these are used to determine the overall match of the sequence to the group of motifs and the probable order and spacing of occurrences of the motifs in the sequence.

Algorithm

Please read the file README distributed with the original MEME.

Usage

Here is a sample session with emast 


% emast ex1.html ex1.out 
Motif detection
Print results for sequences with E-value [10]: 
Show motif matches with p-value < mt [0.0001]:

Go to the input files for this example
Go to the output files for this example

EXAMPLES:

Please note the examples below are unedited excerpts of the original MEME documentation. Bear in mind the EMBASSY and original MEME options may differ in practice (see "1. Command-line arguments").

The following examples assume that file "meme.results" is the output of a MEME run containing at least 3 motifs and file SwissProt is a copy of the Swiss-Prot database on your local disk. DNA_DB is a copy of a DNA database on your local disk.

1) Annotate the training set:
mast meme.results

2) Find sequences matching the motif and annotate them in the SwissProt database:
mast meme.results -d SwissProt

3) Show sequences with weaker combined matches to motifs.
mast meme.results -d SwissProt -ev 200

4) Indicate weaker matches to single motifs in the annotation so that sequences with weak matches to the motifs (but perhaps with the "correct" order and spacing) can be seen:
mast meme.results -d SwissProt -w

5) Include a nominal order and spacing of the first three motifs in the calculation of the sequence p-values to increase the sensitivity of the search for matching sequences:
mast meme.results -d SwissProt -diag "9-[2]-61-[1]-62-[3]-91"

6) Use only the first and third motifs in the search:
mast meme.results -d SwissProt -m 1 -m 3

7) Use only the first two motifs in the search:
mast meme.results -d SwissProt -c 2

8) Search DNA sequences using protein motifs, adjusting p-values and E-values for each sequence by that sequence's composition:
mast meme.results -d DNA_DB -dna -comp

Command line arguments

Where possible, the same command-line qualifier names and parameter order is used as in the original mast. There are however several unavoidable differences and these are clearly documented in the "Notes" section below.

Most of the options in the original mast are given in ACD as "advanced" or "additional" options. -options must be specified on the command-line in order to be prompted for a value for "additional" options but "advanced" options will never be prompted for.

Please note that one only of -stdin or -d should be specified. If you set both, then -d will be used. This behaviour could have been enforced at the level of the ACD file by using an ACD select: or list: type but this would have been inconsistent with the original meme, which has two separate options. 

   Standard (Mandatory) qualifiers:
  [-mfile]             infile     If -d  is not given, MAST looks
                                  for database specified inside of .
   -ev                 float      [10] Print results for sequences with
                                  E-value (Any numeric value)
   -mt                 float      [0.0001] Show motif matches with p-value <
                                  mt (Any numeric value)
  [-outfile]           outfile    [*.emast] MAST program output file

   Additional (Optional) qualifiers:
   -d                  infile     If -d  is not given, MAST looks
                                  for database specified inside of .
   -a                  infile     Input file  is assumed to contain
                                  motifs in the format output by
                                  bin/make_logodds and  is their alphabet;
                                  -d  or -stdin must be specified
                                  when this option is used.
   -bfile              infile     The random model uses the letter frequencies
                                  given in  instead of the
                                  non-redundant database frequencies. The
                                  format of  is the same as that for
                                  the MEME -bfile opton; see the MEME
                                  documentation for details. Sample files are
                                  given in directory tests: tests/nt.freq and
                                  tests/na.freq in the MEME distribution.)
   -smax               integer    [-1] Print results for no more than 
                                  sequences (Any integer value)
   -stdin              boolean    [N] The default is to read the database
                                  specified inside .
   -text               boolean    [N] Default is hypertext (HTML) format
   -dna                boolean    [N] Translate DNA sequences to protein
   -comp               boolean    [N] The random model uses the letter
                                  frequencies in the current target sequence
                                  instead of the non-redundant database
                                  frequencies. This causes p-values and
                                  E-values to be compensated individually for
                                  the actual composition of each sequence in
                                  the database. This option can increase
                                  search time substantially due to the need to
                                  compute a different score distribution for
                                  each high-scoring sequence.
   -rank               integer    [-1] Print results starting with  best
                                  (Any integer value)
   -best               boolean    [N] Include only the best motif in diagrams
   -remcorr            boolean    [N] Remove highly correlated motifs from
                                  query
   -brief              boolean    [N] Brief output: do not print
                                  documentation.
   -b                  boolean    [N] Print only sections I and II
   -nostatus           boolean    [N] Do not print progress report
   -hitlist            boolean    [N] If you specify the -hitlist switch to
                                  MAST, the motif 'diagram' takes the form of
                                  a comma separated list of motif occurrences
                                  ('hits'). Each 'hit' has the format:
                                     
                                  where  is the strand (+ or - for
                                  DNA, blank for protein),  is the
                                  motif number,  is the starting
                                  position of the hit,  is the ending
                                  position of the hit, and  is the
                                  position p-value of the hit.

   Advanced (Unprompted) qualifiers:
   -c                  integer    [-1] Only use the first  motifs (Any
                                  integer value)
   -sep                boolean    [N] Score reverse complement DNA strand as a
                                  separate sequence
   -norc               boolean    [N] Do not score reverse complement DNA
                                  strand
   -w                  boolean    [N] Show weak matches (mt as motif file name. (Any string
                                  is accepted)
   -df                 string     Print  as database name. (Any string is
                                  accepted)
   -minseqs            integer    [-1] Lower bound on number of sequences in
                                  db (Any integer value)
   -mev                float      [-1] Use only motifs with E-values less than
                                   (Any numeric value)
   -m                  integer    [-1] Overrides value set by using -mev. (Any
                                  integer value)
   -diag               string     See on-line documentation for a valid
                                  example. (Any string is accepted)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers Allowed values Default
[-mfile]
(Parameter 1)		 If -d is not given, MAST looks for database specified inside of . Input file Required
-ev Print results for sequences with E-value Any numeric value 10
-mt Show motif matches with p-value < mt Any numeric value 0.0001
[-outfile]
(Parameter 2)		 MAST program output file Output file  
Additional (Optional) qualifiers Allowed values Default
-d If -d is not given, MAST looks for database specified inside of . Input file Required
-a Input file is assumed to contain motifs in the format output by bin/make_logodds and is their alphabet; -d or -stdin must be specified when this option is used. Input file Required
-bfile The random model uses the letter frequencies given in instead of the non-redundant database frequencies. The format of is the same as that for the MEME -bfile opton; see the MEME documentation for details. Sample files are given in directory tests: tests/nt.freq and tests/na.freq in the MEME distribution.) Input file Required
-smax Print results for no more than sequences Any integer value -1
-stdin The default is to read the database specified inside . Boolean value Yes/No No
-text Default is hypertext (HTML) format Boolean value Yes/No No
-dna Translate DNA sequences to protein Boolean value Yes/No No
-comp The random model uses the letter frequencies in the current target sequence instead of the non-redundant database frequencies. This causes p-values and E-values to be compensated individually for the actual composition of each sequence in the database. This option can increase search time substantially due to the need to compute a different score distribution for each high-scoring sequence. Boolean value Yes/No No
-rank Print results starting with best Any integer value -1
-best Include only the best motif in diagrams Boolean value Yes/No No
-remcorr Remove highly correlated motifs from query Boolean value Yes/No No
-brief Brief output: do not print documentation. Boolean value Yes/No No
-b Print only sections I and II Boolean value Yes/No No
-nostatus Do not print progress report Boolean value Yes/No No
-hitlist If you specify the -hitlist switch to MAST, the motif 'diagram' takes the form of a comma separated list of motif occurrences ('hits'). Each 'hit' has the format: where is the strand (+ or - for DNA, blank for protein), is the motif number, is the starting position of the hit, is the ending position of the hit, and is the position p-value of the hit. Boolean value Yes/No No
Advanced (Unprompted) qualifiers Allowed values Default
-c Only use the first motifs Any integer value -1
-sep Score reverse complement DNA strand as a separate sequence Boolean value Yes/No No
-norc Do not score reverse complement DNA strand Boolean value Yes/No No
-w Show weak matches (mt Boolean value Yes/No No
-seqp The default is to use POSITION p-values. Boolean value Yes/No No
-mf Print as motif file name. Any string is accepted An empty string is accepted
-df Print as database name. Any string is accepted An empty string is accepted
-minseqs Lower bound on number of sequences in db Any integer value -1
-mev Use only motifs with E-values less than Any numeric value -1
-m Overrides value set by using -mev. Any integer value -1
-diag See on-line documentation for a valid example. Any string is accepted An empty string is accepted

Input file format

emast reads any normal sequence USAs.

Input files for usage example

File: ex1.html

MEME