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General Discussion / Re: TB binding site binding affinity compared to mutant
« on: October 01, 2019, 09:16:05 pm »
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2
General Discussion / Re: TB binding site binding affinity compared to mutant
« on: September 18, 2019, 09:36:42 pm »
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
Unfortunately, I do not know how to calculate the change in binding affinity between wild and mutated sites of a TF binding site. Currently, the REDUCE Suite is command-line based only, no web interface to it.
Best regards,
Xiang-Jun
Unfortunately, I do not know how to calculate the change in binding affinity between wild and mutated sites of a TF binding site. Currently, the REDUCE Suite is command-line based only, no web interface to it.
Best regards,
Xiang-Jun
3
General Discussion / Re: ddG LogoGenerator
« on: July 12, 2019, 06:17:36 pm »Quote
'm curious about the math behind PWM logos with ddG on the y axis.
The ddG is calculated from PSAM via a simple log-transformation. See the source code in file LogoGenerator.c. You may find the thread "IC from PSAM" informative, especially the summary post at the end from Dr. Bussemaker.
Quote
The LogoGenerator docs suggest I need a PSAM file or multiple sequence alignment to generate this kind of plot, but all I have is a PWM for each transcription factor.
Is it possible to generate a figure like the one above directly from a PWM? Could you point me towards a reference describing how to do this (mathematically)?
With a PWM, you could run Convert2PSAM to transform it into a pseudo-PSAM, and then call LogoGenerator.
HTH,
Xiang-Jun
4
General Discussion / Re: IC from PSAM
« on: May 27, 2019, 10:18:22 pm »Quote
How exactly logoGenerator calculates the height of each nucleotide at each position?
Check the source code. More specifically, the logo_psam() function in LogoGenerator.c. If you can go over a specific example, step-by-step, I'll be able to help.
As for the specifics in the two articles, Harmen may chime in to make a comment.
Best regards,
Xiang-Jun
5
General Discussion / Re: IC from PSAM
« on: May 25, 2019, 10:09:32 am »
Hi Mora,
Thanks for your questions.
Regarding the notation PSAM, please refer to the two MatrixREDUCE-related publications:
You may simply take the PSAM logo as an alternative to the classic information content (IC) type. If you want to dig deep in technical details, please refer to the source code. The LogoGenerator program in the REDUCE Suite is just a tool for users to employ, as they see fit. Notably, it has more options just the IC or PSAM logos.
Hope this helps a bit.
Xiang-Jun
Thanks for your questions.
Regarding the notation PSAM, please refer to the two MatrixREDUCE-related publications:
- "Profiling condition-specific, genome-wide regulation of mRNA stability in yeast." Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80. Epub 2005 Nov 29.
- "Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE." Foat BC, Morozov AV, Bussemaker HJ. Bioinformatics. 2006 Jul 15;22(14):e141-9
You may simply take the PSAM logo as an alternative to the classic information content (IC) type. If you want to dig deep in technical details, please refer to the source code. The LogoGenerator program in the REDUCE Suite is just a tool for users to employ, as they see fit. Notably, it has more options just the IC or PSAM logos.
Hope this helps a bit.
Xiang-Jun
6
General Discussion / Re: LogoGenerator background
« on: May 15, 2019, 09:18:47 pm »
Hi Rocky,
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
The LogoGenerator program simply uses the N-by-4 'PSAM' input data, with possible transformations (ddG, bits_info etc), to create a sequence logo. In essence, the program does not care about nucleotide frequency at each position, other than a log transformation for the ddG style.
To have full control of the logo-generation process, try the '-style=raw' option. You can then generate/edit the input data to LogoGenerator in whatever way that fits your purpose. Note also the Convert2PSAM utility program that may be helpful/convenient for the correct input format.
Hope this helps.
Xiang-Jun
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
The LogoGenerator program simply uses the N-by-4 'PSAM' input data, with possible transformations (ddG, bits_info etc), to create a sequence logo. In essence, the program does not care about nucleotide frequency at each position, other than a log transformation for the ddG style.
To have full control of the logo-generation process, try the '-style=raw' option. You can then generate/edit the input data to LogoGenerator in whatever way that fits your purpose. Note also the Convert2PSAM utility program that may be helpful/convenient for the correct input format.
Hope this helps.
Xiang-Jun
7
General Discussion / Re: "Affinity Profile"
« 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.
Interpretation of the results, however, is beyond my scope of support. Reading publications from the Bussemaker lab may help.
Best regards,
Xiang-Jun
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
8
General Discussion / Re: "Affinity Profile"
« 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
Best regards,
Xiang-Jun
9
General Discussion / Re: Installation of REDUCE SUITE
« on: January 05, 2019, 10:58:32 am »
Thanks for your feedback. As shown in the output of step #4
Best regards,
Xiang-Jun
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
10
General Discussion / Re: Installation of REDUCE SUITE
« 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?
Within the REDUCE-Suite-v2.2/ directory as in step #2, type:
Thanks,
Xiang-Jun
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 perlWithin the REDUCE-Suite-v2.2/ directory as in step #2, type:
Code: [Select]
perl ./bin/REDUCE_Suite_setupThanks,
Xiang-Jun
11
General Discussion / Re: Installation of REDUCE SUITE
« on: January 04, 2019, 02:51:05 pm »
Hi Mina,
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
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
12
General Discussion / Re: "Affinity Profile"
« 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,
Xiang-Jun
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,
Xiang-Jun
13
General Discussion / Re: How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?
« on: September 13, 2018, 09:00:58 pm »
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,
Xiang-Jun
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,
Xiang-Jun
14
General Discussion / Re: Multicollinearity
« on: September 07, 2018, 09:32:52 pm »
Hi,
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
As can be seen from the source code, Transfactivity checks for degeneracy in input data using SVD. However, multicollinearity is not checked by the program, as you already noticed. Users need to deal with the multicollinearity issue using other tools.
Best regards,
Xiang-Jun
Thanks for using the REDUCE Suite and for posting your questions on the Forum.
As can be seen from the source code, Transfactivity checks for degeneracy in input data using SVD. However, multicollinearity is not checked by the program, as you already noticed. Users need to deal with the multicollinearity issue using other tools.
Best regards,
Xiang-Jun
15
General Discussion / Re: download previous versions of REDUCE_Suite
« on: August 16, 2018, 08:44:17 pm »
Hi Kate,
Sorry, no previous versions of the REDUCE_Suite are available for download.
May I know what you want to achieve with the original Convert2PSAM -source=v1 option, possibly with a concrete example?
Xiang-Jun
Sorry, no previous versions of the REDUCE_Suite are available for download.
May I know what you want to achieve with the original Convert2PSAM -source=v1 option, possibly with a concrete example?
Xiang-Jun