
                                   meme 



Function

   Motif detection

Description

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Algorithm

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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

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Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

    Program name                         Description
   antigenic      Finds antigenic sites in proteins
   digest         Protein proteolytic enzyme or reagent cleavage digest
   epestfind      Finds PEST motifs as potential proteolytic cleavage sites
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   oddcomp        Finds protein sequence regions with a biased composition
   patmatdb       Search a protein sequence with a motif
   patmatmotifs   Search a PROSITE motif database with a protein sequence
   pepcoil        Predicts coiled coil regions
   preg           Regular expression search of a protein sequence
   pscan          Scans proteins using PRINTS
   sigcleave      Reports 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.
