Motif Conversion Utilities

The MEME Suite provides tools for conversion to the MEME motif format from other popular motif formats. To use these tools, you need to download and install a local copy of the MEME Suite software.

Program name Input Motif Format
beeml2meme
# cell08_Alx3_3418 UP00108 A 0.12 1.48 0 0 2.18 1.15 0 0.09 0.14 0.13 C 0.02 1.69 1.57 2.2 1.7 0.99 0.82 0.36 0 0.27 G 0.42 2.31 1.9 2.8 2.3 1.12 0.16 0 0.25 0.27 T 0 0 1.67 1.62 0 0 0.59 0.52 0.04 0
chen2meme
>NMYC 13 87 8 9 0 24 90 3 0 117 0 0 88 5 24 0 0 113 4 0 0 0 117 0 0 25 3 89 0 1 116 0 0 13 104 0 3 110 4 0
elm2meme
#"Accession" "ELMIdentifier" "Description" "Regex" "Probability" "#Instances" "#Instances_in_PDB" "ELME000321" "CLV_C14_Caspase3-7" "Caspase-3 and Caspase-7 cleavage site." "[DSTE][^P][^DEWHFYC]D[GSAN]" "0.00309374033071" "39" "0" "ELME000172" "CLV_MEL_PAP_1" "Prophenoloxidase-activating proteinase (PAP) cleavage site ([ILV]-X-X-R-|-[FV]-[GS]-X)." "[ILV]..R[VF][GS]." "0.000105375572148" "12" "0" "ELME000102" "CLV_NRD_NRD_1" "N-Arg dibasic convertase (NRD/Nardilysin) cleavage site (X-|-R-K or R-|-R-X)." "(.RK)|(RR[^KR])" "0.00746473248158" "2" "0" "ELME000101" "CLV_PCSK_FUR_1" "Furin (PACE) cleavage site (R-X-[RK]-R-|-X)." "R.[RK]R." "0.000508722921034" "13" "0" "ELME000108" "CLV_PCSK_KEX2_1" "Yeast kexin 2 cleavage site (K-R-|-X or R-R-|-X)." "[KR]R." "0.007973463544" "1" "0"
iupac2meme
Input is string(s) on the command line.
DNA motif Protein motif
ACGGWNNYCGT
IKLVBZYXXHG
jaspar2meme
Input is directory of files in .pfm, .sites, or .cm format; motif names are taken from file names.
JASPAR 2016 PFM format JASPAR 2014 PFM format OLD PFM format SITES format CM format
>MA0002.1 RUNX1 A [10 12 4 1 2 2 0 0 0 8 13 ] C [ 2 2 7 1 0 8 0 0 1 2 2 ] G [ 3 1 1 0 23 0 26 26 0 0 4 ] T [11 11 14 24 1 16 0 0 25 16 7 ]
>MA0002.1 RUNX1 10 12 4 1 2 2 0 0 0 8 13 2 2 7 1 0 8 0 0 1 2 2 3 1 1 0 23 0 26 26 0 0 4 11 11 14 24 1 16 0 0 25 16 7
10 12 4 1 2 2 0 0 0 8 13 2 2 7 1 0 8 0 0 1 2 2 3 1 1 0 23 0 26 26 0 0 4 11 11 14 24 1 16 0 0 25 16 7
>MA0001 AGL3 1 acaaCCATATATAGtagccactgaat >MA0001 AGL3 2 ccaccCCATATATAGtagtgcgggtggtg
A| 10 4 0 0 0 0 2 85 C| 44 28 0 100 0 0 27 2 G| 27 63 100 0 100 100 69 2 T| 19 4 0 0 0 0 2 10
matrix2meme
1 5 6 3 5 5 5 0 12 1 1 1
nmica2meme
<motif> <name>Abd-B</name> <weightmatrix alphabet="DNA" columns="14"> <column pos="0"> <weight symbol="thymine">0.125</weight> <weight symbol="guanine">0.333333333333333</weight> <weight symbol="cytosine">0.208333333333333</weight> <weight symbol="adenine">0.333333333333333</weight> </column> ... other column tags not shown ... </weightmatrix> <prop><key>PMID</key><value>7914870</value></prop> ... other prop tags not shown ... <threshold>0.0</threshold> </motif>
priority2meme
rna2meme
>micro-rna1 CCAUAUAUAG >micro-rna2 UUUUUUGAUUUAUAG
scpd2meme
>CSRE 0 42 SCPD A 0 0 0 0 0 4 0 1 3 4 1 0 0 T 2 2 0 0 0 0 3 0 0 0 3 1 1 G 1 0 0 4 4 0 0 3 1 0 0 3 3 C 1 2 4 0 0 0 1 0 0 0 0 0 0
sites2meme
Input is a directory of files named Motif ID.txt and a file that maps IDs to alternate names
AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA AAGGTCA CGGGTCA CGGGTCA CGGGTCA GGGGTCG
taipale2meme
"TABLE S1" "MEASURED BINDING PROFILES (DATA FOR FIG1D)" "GLI1" 1 2 3 4 5 6 7 8 9 10 14 "A" 0.010 0.855 0.021 0.000 0.855 0.000 0.124 0.040 0.982 0.287 0.033 "C" 0.001 0.069 0.972 1.000 0.069 1.000 0.876 0.914 0.006 0.518 0.068 "G" 0.973 0.076 0.000 0.000 0.015 0.000 0.000 0.008 0.004 0.097 0.792 "T" 0.016 0.000 0.006 0.000 0.061 0.000 0.000 0.038 0.008 0.098 0.107
tamo2meme
Log-odds matrix for Motif 0 s.CrsGTG (407) # 0 1 2 3 4 5 6 7 #A -0.585 -2.440 -8.672 1.194 -8.672 -3.361 -4.875 -8.672 #C 0.031 0.596 2.121 -4.603 1.909 -0.571 -1.181 -3.243 #T -2.379 0.220 -1.882 -5.256 -2.379 -8.672 1.457 -8.672 #G 1.459 0.571 -1.268 0.533 0.234 2.142 -1.805 2.361 Source: NeuroD1 s.CrsGTG Mono-syllabic 0
transfac2meme
TRANSFAC format TRANSFAC-like format
AC M00001 ID V$MYOD_01 P0 A C G T 01 1 2 2 0 S 02 2 1 2 0 R 03 3 0 1 1 A 04 0 5 0 0 C //
NA JUN.p2 P0 A C G T 1 0.0 71.9 5.1 2321.1 2 6.3 0.6 2368.9 22.3 3 2366.4 3.2 21.9 6.5 4 8.6 2360.2 9.8 19.4 5 430.1 114.1 1836.0 17.7 6 4.8 26.9 1.0 2365.4 7 21.2 2000.6 111.5 264.8 8 2170.8 65.5 54.2 107.5 //
uniprobe2meme
Pou6f1_3733.1 A: 0.380 0.349 0.356 0.229 0.757 0.014 0.984 0.992 C: 0.211 0.309 0.226 0.350 0.046 0.002 0.000 0.001 G: 0.295 0.075 0.169 0.311 0.016 0.000 0.002 0.001 T: 0.112 0.265 0.2473 0.108 0.179 0.982 0.013 0.004