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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
      Note that you *must* register and log in to see the download page.
      Assuming your downloaded tarball is on Mac OS X:

  (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.

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


General Discussion / Re: Installation of REDUCE SUITE
« Last post by shirin on January 05, 2019, 09:17:16 am »
Dear Xiang-Jun
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.

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

/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,

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,
General Discussion / Re: "Affinity Profile"
« Last post by xiangjun on January 01, 2019, 11:46:54 am »
Hi Mina,

Thanks for using the REDUCE Suite and for posting your questions on the Forum.

Type AffinityProfile -h, and try the examples, on how to use the program. PSAM is a MatrixREDUCE-specific term and can be derived from running MatrixREDUCE. You may also run Convert2PSAM to convert commonly-used formats to PSAM. As with AffinityProfile -h, you can type -h or --help of these programs for helpful information with examples.

You may also want to try other (more sophisticated) software tools developed by the Bussemaker Lab.

Best regards,

General Discussion / "Affinity Profile"
« Last post by mina on January 01, 2019, 04:58:35 am »
I am a new user of REDUCE suite.
Is there anybody to help me in using "Affinity Profile". How could we find the PSAM file for our DNA queries to run the computational calculation of binding affinity.

Best Regards,
In the REDUCE Suite, a topology is a shorthand form for exploring a sequence motif, possibly including gaps. It is a flexible and convenient way to test different motif patterns as users see fit in a particular application.

For example, X8 means an 8-mer, with 4^8=65,536 possible combinations of the four canonical DNA or RNA bases. As another example, the topology X3--X4 represents a 7-mer with a 2-nt gap in between. The k-mer size (number of X positions) can be greater than 8: the maximum number is 15. Check the source code for details.

Try the utility program Topo2Dictfile to see a list of sequences corresponding to a given topology. These are the base sequences tested by MotifREDUCE/MatrixREDUCE.

Hope this helps,

General Discussion / How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?
« Last post by mora on September 13, 2018, 04:23:27 pm »
Is topology equal to kmers size of the binding site? what if I want to explore kmer sizes > 8?
General Discussion / Re: Multicollinearity
« Last post by hjb2004 on September 10, 2018, 01:55:26 pm »
Dear Anthony,

Following up on Xiang-Jun's reply, you are correct that the Transfactivity program does not explicitly deal with collinearity. This should not be a problem when Transfactivity is used to infer TF activities for additional expression profiles using one more PSAMs generated by MatrixREDUCE, as the stepwise PSAM discovery implemented by MatrixREDUCE was explicitly designed to make the PSAMs distinct from each other. In other words, when AffinityProfile is used with a set of PSAMs discovered by MatrixREDUCE to create a matrix containing total affinities for each sequence (which is also the first step performed by Transfactivity), the columns of that matrix will be close to orthogonal. The value of the regression coefficients in a multi-PSAM linear regression will then be close those obtained in separate single-PSAM fits.

Things are potentially different, however, when Transfactivity is used with a set of PSAMs obtained from another source such as Jaspar. In that case, there is no guarantee that the columns of the affinity matrix created by AffinityProfile are independent of each other, and the behavior of the regression could indeed become unstable due to collinearity. We were dealing with exactly this situation in two of our lab’s previous papers. In one case, we implemented L2-penalized regression in R with a design matrix generated by AffinityProfile to deal with collinearity when inferring protein-level activities for a large number of yeast transcription factors (Lee et al., Mol Syst Biol 2010; In the second case, when we were doing the same for human transcription factors based on a collection of PWMs from Jaspar, we did some additional preprocessing on the design matrix in R as well (Lee et al., PNAS 2014;; see supplemental methods).

I hope this is useful.

Best regards,
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