meme |
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% 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]: |
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Motif detection Version: EMBOSS:6.4.0.0 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 -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 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 |
|
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 | ||||||||||
-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 | ||||||||||
-[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 | ||||||||||
-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 |
|
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 | ||||||||||
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||
-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 |
>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 |
******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 2.3.1 (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 ******************************************************************************** |
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
eiprscan | Motif detection |
elipop | Prediction of lipoproteins |
emast | Motif detection |
ememe | Multiple EM for Motif Elicitation |
ememetext | Multiple EM for Motif Elicitation. Text file only |
epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
fuzzpro | Search for patterns in protein sequences |
fuzztran | Search for patterns in protein sequences (translated) |
patmatdb | Searches 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 | Scans protein sequence(s) with fingerprints from the PRINTS database |
sigcleave | Reports on signal cleavage sites in a protein sequence |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.