******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2002/04/02 00:11:59) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. 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.sdsc.edu. ******************************************************************************** ******************************************************************************** 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/fang/ppi/new_PPI_032305/memeinput_032405/MEME_YKR067W.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ YNL287W 1.0000 935 YDR238C 1.0000 973 YDL145C 1.0000 1201 YGL137W 1.0000 889 YIL076W 1.0000 359 YFR051C 1.0000 546 ******************************************************************************** ******************************************************************************** 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/fang/ppi/new_PPI_032305/memeinput_032405/MEME_YKR067W.fasta -protein -nmotifs 5 -minw 10 -maxw 300 -minsites 3 -mod zoops -maxsize 1000000 -evt 0.1 model: mod= zoops nmotifs= 5 evt= 0.1 object function= E-value of product of p-values width: minw= 10 maxw= 300 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 3 maxsites= 6 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 em: prior= megap b= 24515 maxiter= 50 distance= 1e-05 data: n= 4903 N= 6 sample: seed= 0 seqfrac= 1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.073 C 0.009 D 0.064 E 0.077 F 0.045 G 0.045 H 0.020 I 0.067 K 0.064 L 0.103 M 0.015 N 0.055 P 0.036 Q 0.040 R 0.038 S 0.080 T 0.059 V 0.068 W 0.010 Y 0.031 Background letter frequencies (from dataset with add-one prior applied): A 0.073 C 0.009 D 0.064 E 0.077 F 0.045 G 0.045 H 0.020 I 0.067 K 0.064 L 0.103 M 0.015 N 0.055 P 0.036 Q 0.040 R 0.038 S 0.080 T 0.059 V 0.068 W 0.011 Y 0.031 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 13 sites = 3 llr = 105 E-value = 1.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::37::: pos.-specific C :::::::a::::: probability D ::::::::::::: matrix E ::7:::::::::: F ::::7:::::7:: G 7:::::::::::: H :a:7:::::::33 I ::::3:::::3:: K ::::::::::::: L :::::3::::::: M :::3::7:::::: N ::3:::::3::3: P ::::::::::::7 Q :::::::::3:3: R 3:::::::::::: S ::::::::::::: T ::::::::::::: V :::::73:3:::: W ::::::::::::: Y ::::::::::::: bits 6.8 * 6.1 * 5.4 * * 4.8 * * * Information 4.1 * * ** * content 3.4 ** ** ** **** (50.7 bits) 2.7 ******** **** 2.0 ************* 1.4 ************* 0.7 ************* 0.0 ------------- Multilevel GHEHFVMCAAFHP consensus R NMILV NQINH sequence V Q -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- YGL137W 138 1.86e-18 NNWALEQTFE GHEHFVMCVAFNP KDPSTFASGC YDL145C 135 1.05e-17 QNRKEIACLT GHNHFVMCAQFHP TDDLIVSASL YDR238C 97 6.57e-11 VPKLAEDGKL RHEMILVCNAIQH DLQHPNEYIR -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YGL137W 1.9e-18 137_[1]_739 YDL145C 1.1e-17 134_[1]_1054 YDR238C 6.6e-11 96_[1]_864 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=3 YGL137W ( 138) GHEHFVMCVAFNP 1 YDL145C ( 135) GHNHFVMCAQFHP 1 YDR238C ( 97) RHEMILVCNAIQH 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 13 n= 4831 bayes= 10.6522 E= 1.1e-003 -159 -182 -239 -280 -398 412 -212 -399 -199 -417 -241 -198 -286 -241 88 -214 -274 -335 -289 -322 -301 -155 -256 -302 -207 -263 528 -388 -303 -311 -162 -106 -277 -45 -111 -243 -252 -329 -173 -30 -255 -313 -95 337 -455 -239 -200 -425 -216 -433 -279 22 -311 -151 -225 -259 -271 -375 -402 -360 -215 -107 -226 -234 -148 -228 492 -238 -202 -197 222 -84 -234 -5 -67 -195 -183 -208 -135 6 -264 -93 -437 -421 400 -348 -261 37 -396 -93 -29 -393 -324 -360 -338 -315 -294 -129 -116 -9 -123 -39 -393 -355 -161 -296 -250 81 -325 88 24 -347 -284 -292 -253 -297 -152 298 -237 -240 -234 -113 -457 -418 -204 -337 -304 -51 -367 -89 548 -391 -349 -331 -321 -338 -237 82 -225 -237 -364 675 -546 -517 -479 -463 -433 -433 -541 -487 -319 -508 -486 -494 -429 -469 -386 -459 -496 -512 180 4 -174 -155 -185 -99 -94 -58 -128 -152 -17 129 -165 -106 -100 -92 -72 189 -184 -161 279 9 -175 -102 -255 -77 -106 -226 -105 -230 -76 -163 -165 180 -81 -68 -109 -116 -224 -216 -264 -93 -437 -421 400 -348 -261 37 -396 -93 -29 -393 -324 -360 -338 -315 -294 -129 -116 -9 -185 -141 -148 -142 -246 -180 401 -316 -129 -272 -105 172 -211 252 -57 -153 -164 -268 -190 -86 -112 -149 -236 -221 -286 -191 232 -302 -184 -281 -173 -218 420 -151 -150 -168 -178 -245 -286 -235 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 13 n= 4831 E= 1.1e-003 0.024293 0.002536 0.012298 0.011003 0.002842 0.777604 0.004620 0.004205 0.016258 0.005725 0.002906 0.013930 0.005010 0.007608 0.070812 0.018184 0.008777 0.006645 0.001427 0.003315 0.009071 0.003055 0.010934 0.009479 0.010655 0.007234 0.780966 0.004520 0.007875 0.011934 0.005010 0.026382 0.005317 0.029674 0.017729 0.014820 0.010225 0.006895 0.003191 0.025038 0.012454 0.001024 0.033395 0.791796 0.001922 0.008540 0.005044 0.003497 0.014395 0.005116 0.002231 0.063670 0.004209 0.014169 0.008097 0.013269 0.008944 0.005031 0.000653 0.002545 0.016481 0.004257 0.013488 0.015185 0.016065 0.009174 0.608071 0.012772 0.015904 0.026283 0.071971 0.030669 0.007188 0.039061 0.024079 0.020648 0.016457 0.016027 0.004131 0.032089 0.011689 0.004685 0.003110 0.004153 0.719567 0.003992 0.003284 0.086024 0.004138 0.054337 0.012602 0.003608 0.003848 0.003334 0.003692 0.008990 0.007601 0.027677 0.004735 0.028931 0.031025 0.006815 0.004227 0.006559 0.014707 0.005755 0.003553 0.116811 0.006772 0.189814 0.018191 0.004966 0.005085 0.005327 0.006651 0.010238 0.020366 0.535248 0.002046 0.005843 0.014372 0.004086 0.002709 0.004232 0.010907 0.004334 0.002447 0.046648 0.005045 0.055504 0.688013 0.003644 0.003237 0.004087 0.004150 0.007662 0.011318 0.119409 0.002216 0.005981 0.005844 0.958750 0.001463 0.002128 0.001618 0.001808 0.001002 0.003321 0.001511 0.003518 0.001694 0.001616 0.001256 0.001317 0.001968 0.003107 0.004042 0.002807 0.000339 0.000890 0.253412 0.009169 0.019331 0.026135 0.012469 0.022482 0.010487 0.044516 0.026489 0.035920 0.013736 0.134161 0.011618 0.019448 0.019144 0.042443 0.035457 0.250538 0.002941 0.010105 0.505910 0.009492 0.019120 0.037871 0.007643 0.026139 0.009618 0.013907 0.031045 0.020907 0.009104 0.017762 0.011564 0.141085 0.021846 0.050010 0.027499 0.030330 0.002241 0.006907 0.011689 0.004685 0.003110 0.004153 0.719567 0.003992 0.003284 0.086024 0.004138 0.054337 0.012602 0.003608 0.003848 0.003334 0.003692 0.008990 0.007601 0.027677 0.004735 0.028931 0.020193 0.003369 0.023135 0.028618 0.008141 0.012835 0.322985 0.007480 0.026312 0.015625 0.007447 0.180137 0.008422 0.232523 0.025851 0.027709 0.018775 0.010574 0.002829 0.017040 0.033553 0.003177 0.012553 0.016551 0.006169 0.011888 0.100359 0.008219 0.017924 0.014723 0.004666 0.012072 0.668519 0.014163 0.013584 0.024948 0.016999 0.012412 0.001459 0.006064 -------------------------------------------------------------------------------- Time 13.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YNL287W 4.05e-01 935 YDR238C 6.31e-08 96_[1(6.57e-11)]_864 YDL145C 1.25e-14 50_[1(3.23e-05)]_29_[1(3.58e-05)]_29_[1(1.05e-17)]_59_[1(2.95e-06)]_31_[1(8.97e-06)]_938 YGL137W 1.63e-15 137_[1(1.86e-18)]_75_[1(6.10e-06)]_651 YIL076W 7.41e-01 359 YFR051C 6.19e-01 546 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because motif E-value > 1.00e-01. ******************************************************************************** CPU: quad.bcf.ku.edu ********************************************************************************