******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.0.0 (Release date: 2008-07-12 05:23:09 +1000 (Sat, 12 Jul 2008)) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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://meme.nbcr.net. ******************************************************************************** ******************************************************************************** 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= /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/lipocalin.s ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ICYA_MANSE 1.0000 189 LACB_BOVIN 1.0000 178 BBP_PIEBR 1.0000 173 RETB_BOVIN 1.0000 183 MUP2_MOUSE 1.0000 180 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/lipocalin.s -text -mod tcm -protein -nostatus -nmotifs 2 -minw 8 model: mod= tcm nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 25 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= megap b= 4515 maxiter= 50 distance= 1e-05 data: n= 903 N= 5 sample: seed= 0 seqfrac= 1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.072 C 0.029 D 0.069 E 0.078 F 0.043 G 0.058 H 0.025 I 0.048 K 0.086 L 0.087 M 0.018 N 0.053 P 0.032 Q 0.029 R 0.031 S 0.059 T 0.048 V 0.070 W 0.017 Y 0.050 Background letter frequencies (from dataset with add-one prior applied): A 0.072 C 0.029 D 0.068 E 0.077 F 0.043 G 0.057 H 0.026 I 0.048 K 0.086 L 0.087 M 0.018 N 0.053 P 0.033 Q 0.029 R 0.031 S 0.059 T 0.048 V 0.069 W 0.017 Y 0.050 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 28 sites = 3 llr = 196 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::3::::::::::::33:7:3::3:a: pos.-specific C ::3:7::::::::::::::::::::::: probability D :7::::3::::33:a::::::::::::: matrix E ::::::3::::3::::::::::::7::: F :::::::3:::::a::::7::::::::: G ::7:::::::::::::::::a::::::: H 3::::::::::::::::::3:::3:::: I :::::::::::::::::::::::::3:: K ::::::::7:3::::3:::::3:::::a L :::::::::::::::3:::::::::::: M :::::::::::::::::::::::::3:: N :::::::::::37::::3:::::::::: P :3:::7:::7:::::::::::::::::: Q :::::::::::::::::::::::::::: R 3::3::::3::::::::3:::::::::: S :::::33:::::::::7::::::::::: T :::::::::::::::::::::3:::::: V ::::3::7:37::::::::::::::3:: W :::::::::::::::3::::::a3:::: Y 3::3::::::::::::::3::::3:::: bits 5.9 * 5.3 * 4.7 * * 4.1 ** * * * Relative 3.5 *** ** * ** *** ** ** Entropy 2.9 ****** **** ********* ****** (94.0 bits) 2.3 **************************** 1.8 **************************** 1.2 **************************** 0.6 **************************** 0.0 ---------------------------- Multilevel HDGACPDVKPVDNFDKSAFAGAWHEIAK consensus RPCRVSEFRVKED LANYH K WAM sequence Y Y S N W R T Y V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------------- BBP_PIEBR 4 1.00e-31 NVY HDGACPEVKPVDNFDWSNYHGKWWEVAK YPNSVEKYGK ICYA_MANSE 5 1.12e-28 GDIF YPGYCPDVKPVNDFDLSAFAGAWHEIAK LPLENENQGK RETB_BOVIN 2 2.70e-21 E RDCRVSSFRVKENFDKARFAGTWYAMAK KDPEGLFLQD -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BBP_PIEBR 1e-31 3_[1]_142 ICYA_MANSE 1.1e-28 4_[1]_157 RETB_BOVIN 2.7e-21 1_[1]_154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=28 seqs=3 BBP_PIEBR ( 4) HDGACPEVKPVDNFDWSNYHGKWWEVAK 1 ICYA_MANSE ( 5) YPGYCPDVKPVNDFDLSAFAGAWHEIAK 1 RETB_BOVIN ( 2) RDCRVSSFRVKENFDKARFAGTWYAMAK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 28 n= 768 bayes= 7.65181 E= 1.5e-004 -179 -268 -226 -205 7 -247 380 -213 -160 -202 -113 -104 -202 11 220 -133 -151 -225 -138 188 -216 -386 335 -73 -371 -240 -199 -326 -279 -356 -267 -75 167 -146 -194 -181 -222 -327 -393 -369 -97 153 -277 -331 -377 372 -289 -325 -338 -381 -261 -219 -262 -254 -205 -136 -211 -295 -366 -400 120 -212 -167 -110 -1 -150 -3 -111 -66 -138 -49 -113 -127 6 261 -52 -65 -115 -143 193 -242 486 -509 -468 -349 -398 -408 -148 -499 -282 -211 -438 -390 -371 -343 -318 -258 -26 -466 -455 -86 -296 -258 -236 -310 -212 -220 -256 -247 -261 -204 -234 440 -128 -144 88 -127 -243 -385 -379 -124 -370 238 171 -329 -166 -121 -272 -136 -285 -178 -50 -167 4 -78 117 -109 -258 -360 -304 -104 -200 -381 -337 167 -306 -235 90 -348 -55 -14 -316 -248 -226 -204 -223 -110 297 -243 -172 -293 -397 -419 -332 -477 -365 -258 -331 325 -383 -273 -289 -326 -157 160 -305 -273 -393 -394 -440 -92 -286 -279 -244 -271 -230 -225 -151 -253 -208 -155 -262 435 -134 -147 -123 -136 62 -362 -352 -77 -211 -273 -202 -213 -253 -181 59 32 -130 -66 -223 -196 -96 -38 -167 -84 301 -304 -294 -192 -391 298 121 -368 -198 -153 -321 -213 -345 -243 113 -236 -74 -148 -134 -178 -317 -388 -346 -246 -359 145 -180 -354 -183 -86 -301 -251 -371 -268 356 -246 -124 -178 -92 -162 -348 -357 -344 -312 -287 -454 -447 429 -406 -331 -187 -472 -135 -135 -414 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-------------------------------------------------------------------------------- [HRY][DP][GC][ARY][CV][PS][DES][VF][KR][PV][VK][DEN][ND]FD[KLW][SA][ANR][FY][AH]G[AKT]W[HWY][EA][IMV]AK -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 42 sites = 2 llr = 218 E-value = 9.9e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::5::::::5::::::::::::5::::5::::::::::: pos.-specific C :::::::::::::::::a:::::::::::::::::::::::: probability D :::::::a::::::::::5:5:a:::::5::::::::::::: matrix E :::::::::::::::::::::5::::::::::::::::::5: F :5:::::::::::::::::::::::::::5:::::::::::: G ::::::::::::::5::::::::::5:::::::::::::::a H ::::::::::::::::::::5:::::a::5:::::::::::: I ::::::::::::5a::::::::::::::5:::5::::::::: K :::::::::a::::::::5::::aa::::::::::5:a:::: L ::::a::::::::::::::::::::::::::::a:::::a:: M :::::::::::::::::::::::::::::::::::::::::: N ::5:::::5:a:::5:5::::::::::::::::::::::::: P :5:::::::::::::::::::5:::::::::::::::::::: Q :::::::::::::::::::::::::::5:::::::::::::: R :::::::::::::::::::::::::::::::::::5:::::: S :::::5:::::::::::::::::::::5::::::a:a::::: T ::::::a:::::::::::::::::::::::::::::::::5: V a::a::::::::::::::::::::::::::5:5:::::a::: W ::5::::::::::::::::::::::::::::a:::::::::: Y ::::::::5::a:::a5::a:::::::::::::::::::::: bits 5.9 * 5.3 * * * 4.7 * * * * * 4.1 * ** ** ** * * * * * * * * * * * * Relative 3.5 ***** ****** * *** ****** ** * * ******* * Entropy 2.9 ****************************************** (157.6 bits) 2.3 ****************************************** 1.8 ****************************************** 1.2 ****************************************** 0.6 ****************************************** 0.0 ------------------------------------------ Multilevel VFNVLATDNKNYAIGYNCDYDEDKKAHQDFAWILSKSKVLEG consensus PW S Y I N Y K HP G SIHV V R T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------ ICYA_MANSE 102 7.93e-48 FKFGQRVVNL VPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEG NTKEVVDNVL BBP_PIEBR 98 4.24e-47 LTYGGVTKEN VFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTG EAKTAVENYL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ICYA_MANSE 7.9e-48 101_[2]_46 BBP_PIEBR 4.2e-47 97_[2]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=42 seqs=2 ICYA_MANSE ( 102) VPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEG 1 BBP_PIEBR ( 98) VFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 42 n= 698 bayes= 8.44294 E= 9.9e-004 -79 -197 -355 -318 -210 -299 -268 107 -341 -110 -67 -322 -234 -238 -197 -229 -101 331 -339 -344 -137 -239 -277 -259 326 -239 -146 -122 -264 -107 -86 -234 308 -139 -142 -141 -155 -151 -95 -24 -243 -321 -175 -279 -121 -223 -96 -239 -261 -226 -172 228 -262 -131 -126 -166 -184 -265 489 -152 -79 -197 -355 -318 -210 -299 -268 107 -341 -110 -67 -322 -234 -238 -197 -229 -101 331 -339 -344 -232 -281 -423 -355 -89 -354 -279 14 -351 312 78 -355 -259 -193 -199 -277 -203 -82 -245 -269 260 -124 -231 -211 -237 -73 -197 -179 -228 -221 -115 -161 -123 -111 -115 215 18 -110 -289 -286 -115 -208 -264 -265 -263 -222 -217 -136 -243 -236 -102 -136 -191 -130 -130 78 380 -138 -309 -322 -283 -407 363 -98 -394 -295 -235 -352 -376 -398 -307 -82 -341 -233 -263 -250 -296 -363 -401 -396 -147 -254 -80 -171 21 -153 82 -155 -172 -189 -105 285 -177 -52 -64 -70 -102 -191 -74 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-123 29 -40 -20 180 -162 -288 -264 -158 -352 -261 -321 -404 391 -289 -372 -331 -425 -294 -212 -283 -265 -201 -180 -272 -356 -365 -412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 42 nsites= 2 E= 9.9e-004 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- V[FP][NW]VL[AS]TD[NY]KNY[AI]I[GN]Y[NY]C[DK]Y[DH][EP]DKK[AG]H[QS][DI][FH][AV]W[IV]LS[KR]SKVL[ET]G -------------------------------------------------------------------------------- Time 6.43 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ICYA_MANSE 3.48e-69 4_[1(1.12e-28)]_69_[2(7.93e-48)]_46 LACB_BOVIN 6.18e-03 12_[1(4.84e-05)]_138 BBP_PIEBR 1.38e-71 3_[1(1.00e-31)]_66_[2(4.24e-47)]_34 RETB_BOVIN 1.91e-18 1_[1(2.70e-21)]_154 MUP2_MOUSE 5.12e-02 180 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************