EMBOSS: meme

meme

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

Motif detection

Description

EMBASSY MEME is a port of the original meme v3.0.1 applications written by Timothy Bailey.

Algorithm

Please read the file README distributed with the original MEME.

Usage

Here is a sample session with omeme

% omeme -protein Motif detection Input sequence(s): memepep.dat Motif Distribution oops : Oops Distribution zoops : Zoops Distribution tcm : TCM Distribution Model to use [zoops]: Maximum number of motifs to find [1]: 3 MEME program output file [carp_rhich.omeme]:

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

Command line arguments

Motif detection
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -model              menu       [zoops] Model to use (Values: oops (Oops
                                  Distribution); zoops (Zoops Distribution);
                                  tcm (TCM Distribution))
   -nmotifs            integer    [1] Maximum number of motifs to find (Any
                                  integer value)
  [-outfile]           outfile    [*.omeme] MEME program output file

   Additional (Optional) qualifiers:
   -ntype              menu       [pair] Method to use (Values: pair (Pairwise
                                  method); blend (Blending method))
   -protein            boolean    [N] Assume sequences are proteins
   -nucleic            boolean    [N] Assume sequences are DNA
   -palindromes        boolean    [N] Allow palindromes
   -ponly              boolean    [N] Force palindromes
   -[no]shorten        boolean    [Y] Allow motifs shorter than MINW
   -nsites             float      [0.] Expected number of sites for each motif
                                  (Any numeric value)
   -minsites           float      [0.] Minimum number of sites for each motif
                                  (Any numeric value)
   -maxsites           float      [0.] Maximum number of sites for each motif
                                  (Any numeric value)
   -w                  integer    [0] Starting motif width to try (Any integer
                                  value)
   -minw               integer    [8] Minimum starting motif width to try (Any
                                  integer value)
   -maxw               integer    [57] Maximum starting motif width to try
                                  (Any integer value)
   -prior              menu       [dirichlet] Prior to use (Values: dirichlet
                                  (Dirichlet prior); dmix (dmix prior); mega
                                  (mega prior); megap (megap prior); addone
                                  (addone prior))
   -[no]brief          boolean    [Y] Don't print documentation
   -b                  float      [-1.0] Strength of the prior (Any numeric
                                  value)
   -spmap              menu       [uni] Mapping start (Values: uni (uni map
                                  type); pam (pam map type))
   -spfuzz             float      [-1.0] Fuzziness of sequence to theta
                                  mapping (Any numeric value)
   -maxiter            integer    [50] Maximum EM iterations to run (Any
                                  integer value)
   -distance           float      [1e-3] EM convergence criterion (Any numeric
                                  value)
   -cons               string     Consensus sequence to start EM from (Any
                                  string)
   -chi                float      [1.0] Cutoff for p-value (Any numeric value)
   -adj                menu       [root] Type (Values: none (no LRT); bon (bon
                                  LRT); root (root LRT))
   -maxsize            integer    [100000] Maximum dataset size in characters
                                  (Any integer value)
   -page               integer    [80] Width of page (Any integer value)
   -status             boolean    [N] Print progress reports
   -v                  boolean    [N] Verbose mode
   -cfive              boolean    [N] Use 5' to 3' complementary strand as
                                  well
   -cthree             boolean    [N] Use 3' to 5' complementary strand as
                                  well
   -wthree             boolean    [N] Use 3' to 5' main strand as well
   -prob               float      [1.0] Starting point confidence level (Any
                                  numeric value)
   -seed               integer    [0] Seed for random numbers in sampling (Any
                                  integer value)
   -seqfrac            float      [1.0] Fraction of sequences to use (Any
                                  numeric value)
   -[no]align          boolean    [Y] Print aligned motif occurrences
   -trace              boolean    [N] Trace starting points
   -allprint           boolean    [N] Print all debugging information
   -wprint             boolean    [N] Print erasure matrix
   -zprint             boolean    [N] Print missing information matrix
   -llprint            boolean    [N] Print log likelihood during EM
   -startsprint        boolean    [N] Print starting points
   -fastaprint         boolean    [N] Print sites in FASTA format
   -timer              integer    [0] Timer type (Any integer value)

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1) seqall Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required

-model list Model to use
oops (Oops Distribution)
zoops (Zoops Distribution)
tcm (TCM Distribution)
zoops

-nmotifs integer Maximum number of motifs to find Any integer value 1

[-outfile]
(Parameter 2) outfile MEME program output file Output file <*>.omeme

Additional (Optional) qualifiers

-ntype list Method to use
pair (Pairwise method)
blend (Blending method)
pair

-protein boolean Assume sequences are proteins Boolean value Yes/No No

-nucleic boolean Assume sequences are DNA Boolean value Yes/No No

-palindromes boolean Allow palindromes Boolean value Yes/No No

-ponly boolean Force palindromes Boolean value Yes/No No

-[no]shorten boolean Allow motifs shorter than MINW Boolean value Yes/No Yes

-nsites float Expected number of sites for each motif Any numeric value 0.

-minsites float Minimum number of sites for each motif Any numeric value 0.

-maxsites float Maximum number of sites for each motif Any numeric value 0.

-w integer Starting motif width to try Any integer value 0

-minw integer Minimum starting motif width to try Any integer value 8

-maxw integer Maximum starting motif width to try Any integer value 57

-prior list Prior to use
dirichlet (Dirichlet prior)
dmix (dmix prior)
mega (mega prior)
megap (megap prior)
addone (addone prior)
dirichlet

-[no]brief boolean Don't print documentation Boolean value Yes/No Yes

-b float Strength of the prior Any numeric value -1.0

-spmap list Mapping start
uni (uni map type)
pam (pam map type)
uni

-spfuzz float Fuzziness of sequence to theta mapping Any numeric value -1.0

-maxiter integer Maximum EM iterations to run Any integer value 50

-distance float EM convergence criterion Any numeric value 1e-3

-cons string Consensus sequence to start EM from Any string

-chi float Cutoff for p-value Any numeric value 1.0

-adj list Type
none (no LRT)
bon (bon LRT)
root (root LRT)
root

-maxsize integer Maximum dataset size in characters Any integer value 100000

-page integer Width of page Any integer value 80

-status boolean Print progress reports Boolean value Yes/No No

-v boolean Verbose mode Boolean value Yes/No No

-cfive boolean Use 5' to 3' complementary strand as well Boolean value Yes/No No

-cthree boolean Use 3' to 5' complementary strand as well Boolean value Yes/No No

-wthree boolean Use 3' to 5' main strand as well Boolean value Yes/No No

-prob float Starting point confidence level Any numeric value 1.0

-seed integer Seed for random numbers in sampling Any integer value 0

-seqfrac float Fraction of sequences to use Any numeric value 1.0

-[no]align boolean Print aligned motif occurrences Boolean value Yes/No Yes

-trace boolean Trace starting points Boolean value Yes/No No

-allprint boolean Print all debugging information Boolean value Yes/No No

-wprint boolean Print erasure matrix Boolean value Yes/No No

-zprint boolean Print missing information matrix Boolean value Yes/No No

-llprint boolean Print log likelihood during EM Boolean value Yes/No No

-startsprint boolean Print starting points Boolean value Yes/No No

-fastaprint boolean Print sites in FASTA format Boolean value Yes/No No

-timer integer Timer type Any integer value 0

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-sequence" associated seqall qualifiers

-sbegin1
-sbegin_sequence integer Start of each sequence to be used Any integer value 0

-send1
-send_sequence integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequence boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequence boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequence boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequence boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequence boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequence boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequence boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequence boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequence string Input sequence format Any string

-iquery1
-iquery_sequence string Input query fields or ID list Any string

-ioffset1
-ioffset_sequence integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequence string Database name Any string

-sid1
-sid_sequence string Entryname Any string

-ufo1
-ufo_sequence string UFO features Any string

-fformat1
-fformat_sequence string Features format Any string

-fopenfile1
-fopenfile_sequence string Features file name Any string

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Input file format

meme reads any normal sequence USAs.

Input files for usage example

File: memepep.dat

>CARP_RHICH P06026 RHIZOPUSPEPSIN PRECURSOR (EC 3.4.23.21)
MKFTLISSCIAIAALAVAVDAAPGEKKISIPLAKNPNYKPSAKNAIQKAIAKYNKHKINT
STGGIVPDAGVGTVPMTDYGNDVEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCG
SRQTKYDPKQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAA
SFANGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKASNGGGGEYIFG
GYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNVAA
SVARAYGASDNGDGTYTISCDTSRFKPLVFSINGASFQVSPDSLVFEEYQGQCIAGFGYG
NFDFAIIGDTFLKNNYVVFNQGVPEVQIAPVAQ
>CARP_YEAST P07267 SACCHAROPEPSIN PRECURSOR (EC 3.4.23.25) (ASPARTATE PROTEASE)
MFSLKALLPLALLLVSANQVAAKVHKAKIYKHELSDEMKEVTFEQHLAHLGQKYLTQFEK
ANPEVVFSREHPFFTEGGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSN
ECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAE
ATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTE
NGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLI
TLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGS
CISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI
>CATD_HUMAN P07339 CATHEPSIN D PRECURSOR (EC 3.4.23.5)
MQPSSLLPLALCLLAAPASALVRIPLHKFTSIRRTMSEVGGSVEDLIAKGPVSKYSQAVP
AVTEGPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIH
HKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQSASSASALGGVKVERQVFG
EATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQQKLVDQNIFSFYLSRDPDAQ
PGGELMLGGTDSKYYKGSLSYLNVTRKAYWQVHLDQVEVASGLTLCKEGCEAIVDTGTSL
MVGPVDEVRELQKAIGAVPLIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQ
AGKTLCLSGFMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAARL
>CHYM_BOVIN P00794 PROCHYMOSIN A AND B PRECURSORS (EC 3.4.23.4) (PREPRORENNIN)
MRCLVVLLAVFALSQGTEITRIPLYKGKSLRKALKEHGLLEDFLQKQQYGISSKYSGFGE
VASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRK
SSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGI
LGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHW
VPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQ
YGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVF
IREYYSVFDRANNLVGLAKAI
>PEPA_ASPAW P17946 ASPERGILLOPEPSIN A PRECURSOR (EC 3.4.23.18)
MVVFSKTAALVLGLSSAVSAAPAPTRKGFTINQIARPANKTRTINLPGMYARSLAKFGGT
VPQSVKEAASKGSAVTTPQNNDEEYLTPVTVGKSTLHLDFDTGSADLWVFSDELPSSEQT
GHDLYTPSSSATKLSGYTWDISYGDGSSASGDVYRDTVTVGGVTTNKQAVEAASKISSEF
VQNTANDGLLGLAFSSINTVQPKAQTTFFDTVKSQLDSPLFAVQLKHDAPGVYDFGYIDD
SKYTGSITYTDADSSQGYWGFSTDGYSIGDGSSSSSGFSAIADTGTTLILLDDEIVSAYY
EQVSGASGETEAGGYVFSCSTNPPDFTVVIGDYKAVVPGKYINYAPISTGSSTCFGGIQS
NSGLGLSILGDVFLKSQYVVFNSEGPKLGFAAQA

Output file format

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

Output files for usage example

File: carp_rhich.omeme

********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 2.3.1.650 (Release date: 2000/11/05 21:47:56)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://www.sdsc.edu/MEME.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://www.sdsc.edu/MEME.
********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
********************************************************************************
********************************************************************************
TRAINING SET
********************************************************************************
DATAFILE= ../../data/memepep.dat (deleted by web version of MEME)
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name           Weight Length  Sequence name           Weight Length  
-------------           ------ ------  -------------           ------ ------  
CARP_RHICH              1.0000    393  CARP_YEAST              1.0000    405  
CATD_HUMAN              1.0000    412  CHYM_BOVIN              1.0000    381  
PEPA_ASPAW              1.0000    394  
********************************************************************************



********************************************************************************
MOTIF  1		width =   8	sites =  5.0
********************************************************************************
Simplified     A  55:2::2:
motif letter-  C  :22:::::
probability    D  ::::::::
matrix         E  ::::::::
               F  ::::::::
               G  ::::::::
               H  ::::332:
               I  2::2::::


  [Part of this file has been deleted for brevity]

letter-probability matrix: alength= 20 w= 16 n= 1910
 0.345527  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.178967  0.009902  0.010727  0.335557  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.842714  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.176047  0.009749  0.515285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.177394  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.844888  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.841956  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.178861  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.176568  0.510727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.840047  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.342714  0.009749  0.515285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.178221  0.003738  0.009380  0.343082  0.015285  0.003844  0.007680  0.008446  0.006793  0.341983  0.012300  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.177057  0.006714  0.011555  0.003738  0.009380  0.176415  0.015285  0.003844  0.174346  0.008446  0.006793  0.175316  0.178967  0.009902  0.010727  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.174346  0.008446  0.173459  0.008650  0.012300  0.009902  0.010727  0.002224  0.505447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.838780 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.345634  0.176568  0.344060  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.006714  0.011555  0.003738  0.176047  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.677394  0.002224  0.005447 
 0.012194  0.003027  0.008623  0.010390  0.673381  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.007680  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.172114 
 0.012194  0.003027  0.508623  0.010390  0.006714  0.011555  0.003738  0.009380  0.009749  0.015285  0.003844  0.341013  0.008446  0.006793  0.008650  0.012300  0.009902  0.010727  0.002224  0.005447 

Stopped because nmotifs = 3 reached.


********************************************************************************
DEBUG INFORMATION
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

model:  mod=         zoops    nmotifs=         3    chi=             1
width:  minw=            8    maxw=           57    shorten=       yes
lambda: minsites=        0    maxsites=        5
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=               1    maxiter=        50
        distance=    0.001
data:   n=            1985    N=               5
strands:    w53
sample: seed=            0    seqfrac=         1
LRT:    adj=          root
Letter frequencies:
A 0.074 C 0.014 D 0.061 E 0.039 F 0.048 G 0.100 H 0.013 I 0.058 K 0.052 
L 0.084 M 0.014 N 0.040 P 0.048 Q 0.042 R 0.021 S 0.094 T 0.072 V 0.069 
W 0.010 Y 0.049 
Non-redundant database letter frequencies:
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
W 0.013 Y 0.033 
Effective length of alphabet = 20
Entropy of dataset (bits) =     -4.1

meme -protein 
********************************************************************************

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
antigenic	Find antigenic sites in proteins
eiprscan	Motif detection
elipop	Predict lipoproteins
emast	Motif detection
ememe	Multiple EM for motif elicitation
ememetext	Multiple EM for motif elicitation, text file only
epestfind	Find PEST motifs as potential proteolytic cleavage sites
fuzzpro	Search for patterns in protein sequences
fuzztran	Search for patterns in protein sequences (translated)
patmatdb	Search protein sequences with a sequence motif
patmatmotifs	Scan a protein sequence with motifs from the PROSITE database
preg	Regular expression search of protein sequence(s)
pscan	Scan protein sequence(s) with fingerprints from the PRINTS database
sigcleave	Report on signal cleavage sites in a protein sequence

Author(s)

This program is an EMBOSS conversion of a program written by Thomas L. Bailey as part of the MEME package.

History

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: memepep.dat

Output file format

Output files for usage example

File: carp_rhich.omeme

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments