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11
General Discussion / Re: "Affinity Profile"
« Last post by xiangjun on February 22, 2019, 11:05:11 am »
Hi Azadeh,

I'm glad to hear that you have got the REDUCE Suite up and running.

Quote
Could you please help me to understand these results ?
What is this matrix  "aff_psam_001.xml" ?
How could I obtain more details on the affinity change and dynamics of binding site ?

Interpretation of the results, however, is beyond my scope of support. Reading publications from the Bussemaker lab may help.

Best regards,

Xiang-Jun

12
General Discussion / Re: "Affinity Profile"
« Last post by azadeh.s on February 22, 2019, 10:15:54 am »
Hello

I'am also novice for using your great package REDUCE_Suit.
I'm interested to study the affinity profile for a vary famous gene COL1A1( I downloded COL1A1 from Ensembel database) I tried to understand the dynamic of affinity profile for a transcription factor Sp1 through its binding site for both wild and mutant COL1A1 genes .

To start my study I ran the commande :
AffinityProfile \
   -prefix=aff_ \
   -threshold=0 \
   -psam=../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml \
   -sequence=sequence_COL1A1.fasta

As a Psam matrix, I used the matrix given in your example.
But then I don't understand the result.

cat seq_psam.dat
   psam_001.xml
NM_000088.3   0.0301094
####################
cat AffinityProfile.log
sequence file: sequence_COL1A1.fasta   cut-off: 0
reading in sequences from file [sequence_COL1A1.fasta]
reading in PSAM ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml [1/1]
[  1]: ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml (forward); pmax=0.025626

Time used: 00:00:00:00

#################
cat aff_psam_001.xml

NM_000088.3   0.0301094   1:2.78962e-104   2:2.8034e-101   3:2.508e-07   4:2.97891e-94   5:3.73255e-103   6:4.75891e-116   7:6.73541e-70   8:6.52039e-71   9:5.81238e-65   10:4.04049e-53   11:9.0064e-52   12:2.29734e-51   13:1.30952e-52   14:1.14509e-48   15:2.33791e-51   16:6.36074e-41   17:4.78319e-46   18:9.88362e-103   19:1.18759e-104   20:7.56195e-118   21:3.05295e-99   22:1.19914e-103   23:2.68201e-21   24:6.17375e-91   25:6.30612e-151   26:6.59257e-50   27:1.50964e-89   28:1.19137e-86   29:9.42612e-47   30:5.0609e-66   31:3.89768e-149   32:1.41179e-49   33:1.62746e-79   34:2.80803e-108   35:5.26342e-77   36:1.28883e-55   37:4.3514e-24   38:5.40903e-86   39:5.26603e-61   40:2.5533e-83   41:2.91799e-121   42:4.92685e-68   43:1.42043e-72   44:3.66844e-54   45:1.07013e-92   46:2.2805e-56   47:4.31802e-112   48:2.12206e-67   49:4.32273e-65   50:5.36831e-108   51:3.10334e-59   52:5.76347e-71   53:3.189e-74   54:1.16991e-15   55:2.31613e-120   56:4.17858e-69   57:3.11132e-70   58:6.68288e-27   59:1.72033e-105   60:7.81592e-63   61:7.91623e-64   62:9.43495e-63   63:1.05312e-74   64:9.53001e-123   65:2.04295e-66   66:5.71577e-30   67:5.90979e-108   68:8.76473e-54   69:2.51005e-73   70:2.08671e-81   71:9.14769e-38   72:5.51473e-31   73:2.33375e-44   74:1.11588e-46   75:1.80495e-39   76:3.66284e-49   77:1.52272e-44   78:4.28484e-71   79:8.19242e-23   80:7.09162e-57   81:1.31163e-58   82:7.40765e-44   83:1.63155e-65   84:6.85533e-61   85:1.67216e-60   86:3.10819e-77   87:7.99735e-26   88:2.20357e-81   89:2.67345e-53   90:7.94344e-34   91:2.97164e-83   92:5.35325e-70   93:4.00621e-67   94:9.56203e-61   95:8.90908e-50   96:2.06665e-60   97:4.78235e-53   98:2.39696e-50   99:1.73158e-52   100:4.63302e-32   101:1.96568e-84   102:9.10009e-69   103:1.6031e-73   104:8.72453e-44   105:3.37299e-88   106:5.02218e-44   107:1.70837e-107   108:6.30181e-110   109:6.10561e-89   110:6.96046e-35   111:2.86401e-101   112:2.9393e-31   113:4.69209e-129   114:2.34756e-56   115:9.01049e-68   116:3.00809e-54   ...
...
..
...
5906:9.52601e-72   5907:9.93085e-28   5908:1.0446e-76   5909:1.53848e-65   5910:6.02333e-52   5911:2.12289e-43   5912:7.00049e-71   5913:7.89907e-37   5914:8.86224e-60   5915:1.47167e-70


####################
cat   seq_psam.dat
   psam_001.xml
NM_000088.3   0.0301094


#########################

Could you please help me to understand these results ?
What is this matrix  "aff_psam_001.xml" ?
How could I obtain more details on the affinity change and dynamics of binding site ?

Thank you in advance
Best Regards

Azadeh
13
General Discussion / Re: "Affinity Profile"
« Last post by xiangjun on February 11, 2019, 03:07:41 pm »
Please see http://reducesuite.bussemakerlab.org/documentation/affinityprofile/ which you get by "AffinityProfile -h".

Best regards,

Xiang-Jun
14
General Discussion / Re: "Affinity Profile"
« Last post by ElliotRi on February 11, 2019, 08:45:15 am »
What examples of how to use the program are you exactly referring to, Xiang-Jun?
15
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 05, 2019, 10:58:32 am »
Thanks for your feedback. As shown in the output of step #4

Code: [Select]
To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
          --------------------------------------------------------------
            export REDUCE_SUITE='C:/cygwin/home/USER/REDUCE-Suite-v2.2'
            export PATH='C:/cygwin/home/USER/REDUCE-Suite-v2.2/bin':$PATH
          --------------------------------------------------------------

        and then *logout* and *login again* to see the effects.
        (alternatively, you may run the commoand: source ~/.bashrc)

Best regards,

Xiang-Jun
16
General Discussion / Re: Installation of REDUCE SUITE
« Last post by shirin on January 05, 2019, 10:43:42 am »
Hi Xiang-Jun
Many thanks for your quick reply. these are my results. What is your suggestion for me?

1- code "which Perl": the result was "/cygdrive/d/Strawberry/perl/bin/perl"

2- code "perl ./bin/REDUCE_Suite_setup": the result was

$ perl ./bin/REDUCE_Suite_setup
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
To install the REDUCE Suite, do as follows:
  (0) Download the Suite from http://reducesuite.bussemakerlab.org/.
      Note that you *must* register and log in to see the download page.
      Assuming your downloaded tarball is on Mac OS X:
          REDUCE-Suite-v2.2-macosx-intel.tar.gz

  (1) tar zxvf REDUCE-Suite-v2.2-macosx-intel.tar.gz
        This will create a directory named REDUCE-Suite-v2.2/

  (2) cd REDUCE-Suite-v2.2/
        You are now in the REDUCE-Suite-v2.2/ directory

  (3) cd src
     >>> [optional] ONLY IF you compile REDUCE Suite from source <<<
        (3a) make
        (3b) cd ../   # back to REDUCE-Suite-v2.2/, as with step (2)

  (4) bin/REDUCE_Suite_setup
        To run the REDUCE Suite, you need to set up the followings:
          o the environment variable REDUCE_SUITE
          o add $REDUCE_SUITE/bin to your command line search path

        for your 'bash' shell, please add the following into ~/.bashrc:
          --------------------------------------------------------------
            export REDUCE_SUITE='C:/cygwin/home/USER/REDUCE-Suite-v2.2'
            export PATH='C:/cygwin/home/USER/REDUCE-Suite-v2.2/bin':$PATH
          --------------------------------------------------------------

        and then *logout* and *login again* to see the effects.
        (alternatively, you may run the commoand: source ~/.bashrc)

  (5) type MatrixREDUCE -h
           LogoGenerator -h
           HTMLSummary -h
      etc. for command-line help and worked examples

  (6) Note: to use HTMLSummary for the summary page, you need to install
            GhostScript. See $REDUCE_SUITE/config/pkg_settings.cfg for
            setting path to the command 'gs'. LogoGenerator generates
            the logo image in EPS format, and uses 'gs' to convert EPS
            into PDF, PNG, or JPG. Additionally, with ImageMagick, you
            can also get the logo image in GIF.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
17
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 05, 2019, 10:14:32 am »
Hi Shirin,

Sorry to hear your difficult experience in installing the REDUCE Suite. To help fix the issues you have, could you please try the followings and report back what you get?

Code: [Select]
which perl
Within the REDUCE-Suite-v2.2/ directory as in step #2, type:

Code: [Select]
perl ./bin/REDUCE_Suite_setup

Thanks,

Xiang-Jun
18
General Discussion / Re: Installation of REDUCE SUITE
« Last post by shirin on January 05, 2019, 09:17:16 am »
Dear Xiang-Jun
Hi
I have this problem too during the REDUCE suite installation, I have installed Perl "This is Perl 5, version 12, subversion 3 (v5.12.3)" but I face with this error again "-bash: bin/REDUCE_Suite_setup: /usr/bin/perl: bad interpreter: No such file or directory"
I do not know what is the reason and What should I do? could you please kindly help me.

sincerely,
Shirin
19
General Discussion / Re: Installation of REDUCE SUITE
« Last post by xiangjun on January 04, 2019, 02:51:05 pm »
Hi Mina,

Quote
/usr/bin/perl: bad interpreter: No such file or directory

The error message shows that you do not have Perl installed, at least it is not located at /usr/bin/perl.

If the error message or the instructions at "Set up the REDUCE Suite" does not make sense to you, please find a local expert for help.

Best regards,

Xiang-Jun
20
General Discussion / Installation of REDUCE SUITE
« Last post by mina on January 04, 2019, 11:09:29 am »
Dear Friends,
We have been trying to install REDUCE Suite in windows (Cygwin). We have gone toward step 4 in which, unfortunately, we receive the following error:
$ ./bin/REDUCE_Suite_setup
-bash: ./bin/REDUCE_Suite_setup: /usr/bin/perl: bad interpreter: No such file or directory

Could you please kindly give us advice on how to manage this problem?
Best Regards,
Mina
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