meme.farntrans5.zoops

来自「EM算法的改进」· ZOOPS 代码 · 共 476 行 · 第 1/3 页

ZOOPS
476 行
字号
123
********************************************************************************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 zoops -protein -nostatus -nmotifs 2 model:  mod=         zoops    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=        5    wnsites=       0.8theta:  prob=            1    spmap=         pam    spfuzz=        120em:     prior=       megap    b=            9500    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----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 1 in BLOCKS format--------------------------------------------------------------------------------BL   MOTIF 1 width=32 seqs=5BET2_YEAST               (  219) QLPEGGLNGRPSKLPDVCYSWWVLSSLAIIGR  1 RATRABGERB               (  223) QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGR  1 PFTB_RAT                 (  282) MRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHR  1 CAL1_YEAST               (  271) QSDDGGFQGRENKFADTCYAFWCLNSLHLLTK  1 RAM1_YEAST               (  292) LQEERGFCGRSNKLVDGCYSFWVGGSAAILEA  1 //----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 1 position-specific scoring matrix--------------------------------------------------------------------------------log-odds matrix: alength= 20 w= 32 n= 1745 bayes= 9.38835 E= 2.1e-031   -200   -366   -346   -115   -278   -398    -55   -204   -204    -76    113   -179   -279    420   -150   -275   -216   -219   -307   -344    -65   -312   -142    -47   -216   -217    -93   -145     45    112    -67    -35   -180    179    174     68    -55   -121   -271   -200
123

meme.farntrans5.zoops - 源码说明

本页面展示了「EM算法的改进」中的 meme.farntrans5.zoops 源码文件，采用 ZOOPS 编程语言编写，共 476 行代码。您可以在线阅读完整代码内容，也可以返回资源详情页下载完整源码包进行本地学习和开发。

虫虫开发者社区收录了大量与EM算法相关的技术资源，包括源代码、技术文档、电路图等，是电子工程师和嵌入式开发者的专业学习平台。

⌨️ 快捷键说明

复制代码Ctrl + C
搜索代码Ctrl + F
全屏模式F11
增大字号Ctrl + =
减小字号Ctrl + -
显示快捷键?