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11
General Discussion / Re: IC from PSAM
« Last post by mora on May 26, 2019, 04:56:22 pm »
Thanks a lot!! One more question:

How exactly logoGenerator calculates the height of each nucleotide at each position?

your Foat et al 2005 paper says that it "the height of each nucleotide is determined by subtracting the smallest weight for any nucleotide at that position and then dividing by the sum of all four weights".

I replicated this on a PSAM I made and the results were similar, but not identical, to the results obtained by Logo nucleotides (y-axis) height.

Does your LogoGenerator makes any other step other than subtracting the smallest weight? maybe some type of normalization?

Ohh I see in your 2006 papers says that for the affinity logo you used the average right? what about when you used the option -style=bits_info? How nucleotide height is calculated then to approximate bits?


12
General Discussion / Re: IC from PSAM
« Last post by xiangjun 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

13
General Discussion / IC from PSAM
« Last post by mora on May 24, 2019, 04:36:26 pm »
What does the information content (IC) from logos built from a PSAM matrix mean? how does this differ from IC inferred from a classic PSSM/PWM matrix?

Also, is there any information about how LogoGenerator calculate the IC in bits from the values in the PSAM? I assume it has to be very different from how it is calculated according to classic PWM right? (see link)
https://en.wikipedia.org/wiki/Position_weight_matrix

 
14
General Discussion / Re: LogoGenerator background
« Last post by xiangjun 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
15
General Discussion / LogoGenerator background
« Last post by mparida on May 15, 2019, 12:04:47 pm »
Hi Xiang-Jun
The algorithm works great. I was able to generate ddG logos using this software. However, I was wondering if the LogoGenerator uses the deviation from the uniform background frequency (A,T,G,C), such as 0.25 to show over-represented and under-represented nucleotide frequency at each position. If so, is there an easy way to change it to the actual background frequency observed from our data instead. For example, instead of assuming the background frequency of A,T,G,C as 0.25 each can we change it to 0.20,0.20,0.30,0.30. Any help in this regard is appreciated.
 
Rocky
16
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

17
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
18
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
19
General Discussion / Re: "Affinity Profile"
« Last post by ElliotRi on February 11, 2019, 08:45:15 am »
Quote from: xiangjun on January 01, 2019, 11:46:54 am
Hi Mina,

Thanks for using the electric log splitters 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

What examples of how to use the program are you exactly referring to, Xiang-Jun?
20
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
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊]. See also http://forum.x3dna.org and http://x3dna.org