📄 meme.lipocalin.tcm
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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/lipocalin.sALPHABET= ACDEFGHIKLMNPQRSTVWYSequence 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 aproblem with the MEME software.command: meme /home/tbailey/tests/lipocalin.s -mod tcm -protein -nostatus -nmotifs 2 model: mod= tcm 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= 2 maxsites= 25 wnsites= 0.8theta: prob= 1 spmap= pam spfuzz= 120em: prior= megap b= 4515 maxiter= 50 distance= 1e-05data: n= 903 N= 5sample: seed= 0 seqfrac= 1Dirichlet mixture priors file: prior30.plibLetter 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 ** * * * Information 3.5 *** ** * ** *** ** **content 2.9 ****** **** ********* ******(94.0 bits) 2.3 **************************** 1.8 **************************** 1.2 **************************** 0.6 **************************** 0.0 ----------------------------Multilevel HDGACPDVKPVDNFDKSAFAGAWHEIAKconsensus 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 1.01e-31 NVY HDGACPEVKPVDNFDWSNYHGKWWEVAK YPNSVEKYGKICYA_MANSE 5 1.13e-28 GDIF YPGYCPDVKPVNDFDLSAFAGAWHEIAK LPLENENQGKRETB_BOVIN 2 2.52e-21 E RDCRVSSFRVKENFDKARFAGTWYAMAK KDPEGLFLQD---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM------------- ---------------- -------------BBP_PIEBR 1e-31 3_[1]_142ICYA_MANSE 1.1e-28 4_[1]_157RETB_BOVIN 2.5e-21 1_[1]_154---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 in BLOCKS format--------------------------------------------------------------------------------BL MOTIF 1 width=28 seqs=3BBP_PIEBR ( 4) HDGACPEVKPVDNFDWSNYHGKWWEVAK 1 ICYA_MANSE ( 5) YPGYCPDVKPVNDFDLSAFAGAWHEIAK 1 RETB_BOVIN ( 2) RDCRVSSFRVKENFDKARFAGTWYAMAK 1 //--------------------------------------------------------------------------------⌨️ 快捷键说明
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