📄 meme.farntrans5.oops
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********************************************************************************MEME - Motif discovery tool********************************************************************************MEME version 3.5.3 (Release date: 2006-03-08 09:30:25 +1000 (Wed, 08 Mar 2006))For further information on how to interpret these results or to geta copy of the MEME software please access http://meme.nbcr.net.This file may be used as input to the MAST algorithm for searchingsequence databases for matches to groups of motifs. MAST is availablefor 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 discovermotifs in biopolymers", Proceedings of the Second InternationalConference on Intelligent Systems for Molecular Biology, pp. 28-36,AAAI Press, Menlo Park, California, 1994.****************************************************************************************************************************************************************TRAINING SET********************************************************************************DATAFILE= /home/tbailey/tests/farntrans5.sALPHABET= ACDEFGHIKLMNPQRSTVWYSequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ RAM1_YEAST 1.0000 431 PFTB_RAT 1.0000 437 BET2_YEAST 1.0000 325 RATRABGERB 1.0000 331 CAL1_YEAST 1.0000 376 ****************************************************************************************************************************************************************COMMAND LINE SUMMARY********************************************************************************This information can also be useful in the event you wish to report aproblem with the MEME software.command: meme /home/tbailey/tests/farntrans5.s -mod oops -protein -nostatus -nmotifs 2 model: mod= oops nmotifs= 2 evt= infobject function= E-value of product of p-valueswidth: minw= 8 maxw= 50 minic= 0.00width: wg= 11 ws= 1 endgaps= yesnsites: minsites= 5 maxsites= 5 wnsites= 0.8theta: prob= 1 spmap= pam spfuzz= 120em: prior= dmix b= 0 maxiter= 50 distance= 1e-05data: n= 1900 N= 5sample: seed= 0 seqfrac= 1Dirichlet mixture priors file: prior30.plibLetter frequencies in dataset:A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057 W 0.018 Y 0.041 Background letter frequencies (from dataset with add-one prior applied):A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057 W 0.018 Y 0.041 ****************************************************************************************************************************************************************MOTIF 1 width = 32 sites = 5 llr = 352 E-value = 2.1e-031********************************************************************************-------------------------------------------------------------------------------- Motif 1 Description--------------------------------------------------------------------------------Simplified A ::::::::::::::2::::2:::22:24:::2pos.-specific C :::::::2::2::::::a::::2:::::::::probability D ::22:::::::::::a::::::::::::::::matrix E ::26::::::22::::::::::::::::::2: F ::2:::6::::::2::::::6::::::::::: G ::::8a::a:::::::4::::::24:::::4: H :::::::::::::::::::::::::::2::2: I ::::::::::::::::::::::::::::64:: K ::::::::::::a::::::::::::::2:::2 L 24::::4::::::8:::::::::6:28:46:: M 2::::::::::::::::::::::::::::::: N :::::::4:::6::::::::::::2::::::: P ::4:::::::4:::4::::::::::::2:::: Q 62:::::4::::::::::::::2::::::::: R :2::2::::a:::::::::::::::::::::6 S :2:2::::::22:::::::8::::28:::::: T ::::::::::::::::2:::::::::::::2: V ::::::::::::::4:4:::::6::::::::: W ::::::::::::::::::::4a:::::::::: Y ::::::::::::::::::a::::::::::::: bits 5.8 * 5.2 * 4.6 * ** * 4.0 * * * ** ** Information 3.5 * ** *** * * ** ** content 2.9 * ******* ***** ****** ** ** *(101.7 bits) 2.3 * ****************************** 1.7 ******************************** 1.2 ******************************** 0.6 ******************************** 0.0 --------------------------------Multilevel QLPEGGFNGRPNKLPDGCYSFWVLGSLAILGRconsensus LQDDR LQ CE FV V AW CAALAHLIEAsequence MRES C ES A T QGN K HK SF S S P T ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value--------------------------------------------------------------------------------Sequence name Start P-value Site ------------- ----- --------- --------------------------------BET2_YEAST 219 6.77e-34 EEIGWWLCER QLPEGGLNGRPSKLPDVCYSWWVLSSLAIIGR LDWINYEKLTRATRABGERB 223 1.47e-32 DLLGWWLCER QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGR LHWIDREKLRPFTB_RAT 282 3.39e-29 SLLQWVTSRQ MRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHR ALHAQGDPALCAL1_YEAST 271 5.02e-27 FESELNASYD QSDDGGFQGRENKFADTCYAFWCLNSLHLLTK DWKMLCQTELRAM1_YEAST 292 5.02e-27 KLLEWSSARQ LQEERGFCGRSNKLVDGCYSFWVGGSAAILEA FGYGQCFNKH---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM------------- ---------------- -------------BET2_YEAST 6.8e-34 218_[1]_75RATRABGERB 1.5e-32 222_[1]_77PFTB_RAT 3.4e-29 281_[1]_124CAL1_YEAST 5e-27 270_[1]_74RAM1_YEAST 5e-27 291_[1]_108----------------------------------------------------------------------------------------------------------------------------------------------------------------⌨️ 快捷键说明
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