meme.crp0.tcm

来自「EM算法的改进」· TCM 代码 · 共 391 行 · 第 1/2 页
TCM
391 行
    13  -1081   -182    101 ----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 1 position-specific probability matrix--------------------------------------------------------------------------------letter-probability matrix: alength= 4 w= 19 nsites= 18 E= 2.8e-004  0.000000  0.222222  0.000000  0.777778  0.000000  0.055556  0.500000  0.444444  0.000000  0.222222  0.000000  0.777778  0.222222  0.000000  0.777778  0.000000  0.666667  0.222222  0.000000  0.111111  0.222222  0.166667  0.277778  0.333333  0.166667  0.555556  0.166667  0.111111  0.222222  0.222222  0.388889  0.166667  0.666667  0.000000  0.166667  0.166667  0.055556  0.277778  0.333333  0.333333  0.222222  0.111111  0.388889  0.277778  0.000000  0.111111  0.000000  0.888889  0.055556  0.944444  0.000000  0.000000  0.833333  0.000000  0.111111  0.055556  0.000000  0.944444  0.000000  0.055556  0.888889  0.000000  0.055556  0.055556  0.333333  0.444444  0.000000  0.222222  0.333333  0.111111  0.000000  0.555556  0.333333  0.000000  0.055556  0.611111 ----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 1 regular expression--------------------------------------------------------------------------------[TC][GT][TC][GA][AC][TGA]C[GAC]A[GTC][GTA]TCACA[CAT][TA][TA]--------------------------------------------------------------------------------Time  3.17 secs.****************************************************************************************************************************************************************MOTIF  2	width =   11   sites =   5   llr = 63   E-value = 4.9e+003********************************************************************************--------------------------------------------------------------------------------	Motif 2 Description--------------------------------------------------------------------------------Simplified        A  :::6aa:::::pos.-specific     C  2::::::2:::probability       G  8:a4::::a:2matrix            T  :a::::a8:a8         bits    2.4   *     *                   2.1   *     *                   1.9   *     *                   1.6 *** *** ** Information      1.4 *** *** ** content          1.2 *** *******(18.2 bits)      0.9 ***********                 0.7 ***********                 0.5 ***********                 0.2 ***********                 0.0 -----------Multilevel           GTGAAATTGTTconsensus            C  G   C  Gsequence                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 sites sorted by position p-value--------------------------------------------------------------------------------Sequence name            Strand  Start   P-value               Site  -------------            ------  ----- ---------            -----------uxu1                         +     10  9.04e-07  CCCATGAGA GTGAAATTGTT GTGATGTGGTlac                          -     95  9.04e-07          . GTGAAATTGTT ATCCGCTCAClac                          +     77  2.07e-06 CGTATGTTGT GTGGAATTGTG AGCGGATAACgale                         -     31  2.07e-06 GAATAAATTA GTGGAATCGTT TACACAAGAAtnaa                         -     94  2.97e-06          T CTGAAATTGTT TAAATGTGAA----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM-------------            ----------------  -------------uxu1                                9e-07  9_[+2]_85lac                               2.1e-06  76_[+2]_7_[-2]gale                              2.1e-06  30_[-2]_64tnaa                                3e-06  93_[-2]_1----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 in BLOCKS format--------------------------------------------------------------------------------BL   MOTIF 2 width=11 seqs=5uxu1                     (   10) GTGAAATTGTT  1 lac                      (   95) GTGAAATTGTT  1 lac                      (   77) GTGGAATTGTG  1 gale                     (   31) GTGGAATCGTT  1 tnaa                     (   94) CTGAAATTGTT  1 //----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 position-specific scoring matrix--------------------------------------------------------------------------------log-odds matrix: alength= 4 w= 11 n= 1710 bayes= 8.66584 E= 4.9e+003   -897      3    203   -897   -897   -897   -897    172   -897   -897    235   -897     98   -897    103   -897    172   -897   -897   -897    172   -897   -897   -897   -897   -897   -897    172   -897      3   -897    139   -897   -897    235   -897   -897   -897   -897    172   -897   -897      3    139 ----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 position-specific probability matrix--------------------------------------------------------------------------------letter-probability matrix: alength= 4 w= 11 nsites= 5 E= 4.9e+003  0.000000  0.200000  0.800000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  1.000000  0.000000  0.600000  0.000000  0.400000  0.000000  1.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.200000  0.000000  0.800000  0.000000  0.000000  1.000000  0.000000  0.000000  0.000000  0.000000  1.000000  0.000000  0.000000  0.200000  0.800000 ----------------------------------------------------------------------------------------------------------------------------------------------------------------	Motif 2 regular expression--------------------------------------------------------------------------------[GC]TG[AG]AAT[TC]GT[TG]--------------------------------------------------------------------------------Time  5.27 secs.****************************************************************************************************************************************************************SUMMARY OF MOTIFS********************************************************************************--------------------------------------------------------------------------------	Combined block diagrams: non-overlapping sites with p-value < 0.0001--------------------------------------------------------------------------------SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM-------------            ----------------  -------------ce1cg                            1.17e-04  16_[-1(5.52e-06)]_28_[+1(5.44e-07)]_23ara                              1.94e-05  57_[+1(2.02e-08)]_29bglr1                            1.81e-03  78_[+1(3.88e-06)]_8crp                              2.53e-03  65_[+1(2.43e-06)]_21cya                              1.15e-03  49_[-1(9.07e-06)]_37deop2                            8.27e-04  9_[+1(2.00e-06)]_31_[-1(1.19e-06)]_27gale                             8.39e-07  30_[-2(2.07e-06)]_3_[+1(6.87e-07)]_42ilv                              1.31e-02  41_[+1(1.92e-05)]_45lac                              4.37e-06  11_[+1(9.07e-06)]_46_[+2(2.07e-06)]_7_[-2(9.04e-07)]male                             1.62e-03  16_[+1(1.47e-06)]_70malk                             6.73e-03  60_[-1(2.06e-05)]_26malt                             1.76e-05  40_[-1(6.87e-07)]_46ompa                             9.97e-04  50_[+1(8.61e-07)]_36tnaa                             1.54e-05  73_[+1(1.06e-05)]_1_[-2(2.97e-06)]_1uxu1                             3.88e-04  9_[+2(9.04e-07)]_85pbr322                           5.63e-03  52_[-1(6.54e-06)]_34trn9cat                          3.22e-01  105tdc                              1.58e-03  78_[+1(6.54e-06)]_8--------------------------------------------------------------------------------****************************************************************************************************************************************************************Stopped because nmotifs = 2 reached.********************************************************************************CPU: chromo.imb.uq.edu.au********************************************************************************
meme.crp0.tcm - 源码说明

本页面展示了「EM算法的改进」中的 meme.crp0.tcm 源码文件，采用 TCM 编程语言编写，共 391 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。
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