meme

 

Function

Motif detection

Description

**************** EDIT HERE ****************

Algorithm

**************** EDIT HERE ****************

Usage

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
   -model              menu       Model to use
   -nmotifs            integer    Maximum number of motifs to find
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -ntype              menu       Method to use
   -protein            boolean    Assume sequences are proteins
   -nucleic            boolean    Assume sequences are DNA
   -palindromes        boolean    Allow palindromes
   -ponly              boolean    Force palindromes
   -[no]shorten        boolean    Allow motifs shorter than MINW
   -nsites             float      Expected number of sites for each motif
   -minsites           float      Minimum number of sites for each motif
   -maxsites           float      Maximum number of sites for each motif
   -w                  integer    Starting motif width to try
   -minw               integer    Minimum starting motif width to try
   -maxw               integer    Maximum starting motif width to try
   -prior              menu       Prior to use
   -[no]brief          boolean    Don't print documemtation
   -b                  float      Strength of the prior
   -spmap              menu       Mapping start
   -spfuzz             float      Fuzziness of sequence to theta mapping
   -maxiter            integer    Maximum EM iterations to run
   -distance           float      EM convergence criterion
   -cons               string     Consensus sequence to start EM from
   -chi                float      Cutoff for p-value
   -adj                menu       Type
   -maxsize            integer    Maximum dataset size in characters
   -page               integer    Width of page
   -status             boolean    Print progress reports
   -v                  boolean    Verbose mode
   -cfive              boolean    Use 5' to 3' complementary strand as well
   -cthree             boolean    Use 3' to 5' complementary strand as well
   -wthree             boolean    Use 3' to 5' main strand as well
   -prob               float      Starting point confidence level
   -seed               integer    Seed for random numbers in sampling
   -seqfrac            float      Fraction of sequences to use
   -[no]align          boolean    Print aligned motif occurrences
   -trace              boolean    Trace starting points
   -allprint           boolean    Print all debugging information
   -wprint             boolean    Print erasure matrix
   -zprint             boolean    Print missing information matrix
   -llprint            boolean    Print log likelihood during EM
   -startsprint        boolean    Print starting points
   -fastaprint         boolean    Print sites in FASTA format
   -timer              integer    Timer type

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
-model Model to use
oops (Oops Distribution)
zoops (Zoops Distribution)
tcm (TCM Distribution)
zoops
-nmotifs Maximum number of motifs to find Any integer value 1
[-outfile]
(Parameter 2)
Output file name Output file <sequence>.meme
Additional (Optional) qualifiers Allowed values Default
-ntype Method to use
pair (Pairwise method)
blend (Blending method)
pair
-protein Assume sequences are proteins Boolean value Yes/No No
-nucleic Assume sequences are DNA Boolean value Yes/No No
-palindromes Allow palindromes Boolean value Yes/No No
-ponly Force palindromes Boolean value Yes/No No
-[no]shorten Allow motifs shorter than MINW Boolean value Yes/No Yes
-nsites Expected number of sites for each motif Any numeric value 0.
-minsites Minimum number of sites for each motif Any numeric value 0.
-maxsites Maximum number of sites for each motif Any numeric value 0.
-w Starting motif width to try Any integer value 0
-minw Minimum starting motif width to try Any integer value 8
-maxw Maximum starting motif width to try Any integer value 57
-prior Prior to use
dirichlet (Dirichlet prior)
dmix (dmix prior)
mega (mega prior)
megap (megap prior)
addone (addone prior)
dirichlet
-[no]brief Don't print documemtation Boolean value Yes/No Yes
-b Strength of the prior Any numeric value -1.0
-spmap Mapping start
uni (uni map type)
pam (pam map type)
uni
-spfuzz Fuzziness of sequence to theta mapping Any numeric value -1.0
-maxiter Maximum EM iterations to run Any integer value 50
-distance EM convergence criterion Any numeric value 1e-3
-cons Consensus sequence to start EM from Any string is accepted An empty string is accepted
-chi Cutoff for p-value Any numeric value 1.0
-adj Type
none (no LRT)
bon (bon LRT)
root (root LRT)
root
-maxsize Maximum dataset size in characters Any integer value 100000
-page Width of page Any integer value 80
-status Print progress reports Boolean value Yes/No No
-v Verbose mode Boolean value Yes/No No
-cfive Use 5' to 3' complementary strand as well Boolean value Yes/No No
-cthree Use 3' to 5' complementary strand as well Boolean value Yes/No No
-wthree Use 3' to 5' main strand as well Boolean value Yes/No No
-prob Starting point confidence level Any numeric value 1.0
-seed Seed for random numbers in sampling Any integer value 0
-seqfrac Fraction of sequences to use Any numeric value 1.0
-[no]align Print aligned motif occurrences Boolean value Yes/No Yes
-trace Trace starting points Boolean value Yes/No No
-allprint Print all debugging information Boolean value Yes/No No
-wprint Print erasure matrix Boolean value Yes/No No
-zprint Print missing information matrix Boolean value Yes/No No
-llprint Print log likelihood during EM Boolean value Yes/No No
-startsprint Print starting points Boolean value Yes/No No
-fastaprint Print sites in FASTA format Boolean value Yes/No No
-timer Timer type Any integer value 0
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

meme reads any normal sequence USAs.

Output file format

meme outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Data files

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
antigenicFinds antigenic sites in proteins
digestProtein proteolytic enzyme or reagent cleavage digest
epestfindFinds PEST motifs as potential proteolytic cleavage sites
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pregRegular expression search of a protein sequence
pscanScans proteins using PRINTS
sigcleaveReports protein signal cleavage sites

Author(s)

[an error occurred while processing this directive]

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.