Recent Posts

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11
Documentation / Re: Other utility programs
« Last post by Millson on July 18, 2018, 07:45:10 am »
Hi Xiangjun, do you have more resources to share on ProcessFASTA? Cheers.
12
General Discussion / Re: availability of FeatureREDUCE?
« Last post by xiangjun on July 17, 2018, 06:58:47 pm »
Thanks for posting your FeatureREDUCE question(s) on the REDUCE Suite Forum. Unfortunately (and as you noticed), FeatureREDUCE is not available from the basic REDUCE Suite which includes MatrixREDUCE/MotifREDUCE and some accessory programs. I was not involved in the development of FeatureREDUCE and its support (if any) is not covered by the Forum (I've made this point clear from the announcement page). Sorry for not being able to provide you with a more positive answer.

Xiang-Jun
13
General Discussion / availability of FeatureREDUCE?
« Last post by pk on July 17, 2018, 05:34:01 pm »
If possible, I'd like to try running FeatureREDUCE (https://doi.org/10.7554/eLife.06397).

The Riley lab points to the older Bussemaker lab "Software" page (http://rileylab.org/featurereduce/), but that appears to be defunct. I assumed I'd be able to download the software from this forum along with the remaining REDUCE software suite. It doesn't appear to be in the downloadable tar balls. Should I not be trying to use FeatureREDUCE to analyze PBM data, i.e. is it excluded from the REDUCE suite for a reason, or am I just not seeing it?

I found a GitHub repo for the project (https://github.com/FeatureREDUCE/FeatureREDUCE), but it appears to be untouched since 2015 (the paper is still listed as "in revision" in the README). Is the GitHub repo the newest/only available implementation?

Thanks for the help!
14
General Discussion / Re: Error when generating logos in PDF format
« Last post by xiangjun on February 11, 2018, 09:53:30 am »
Quote
I can't directly read LogoGenerator-created EPS file on Linux. Am I missing something?

Could you be more specific? Please provide a concrete example so I (and others) can reproduce what you failed to achieve.

Best regards,

Xiang-Jun
15
General Discussion / Re: Error when generating logos in PDF format
« Last post by Rochford on February 11, 2018, 08:59:59 am »
Hi Xiang, just a quick question, I can't directly read LogoGenerator-created EPS file on Linux. Am I missing something?
16
General Discussion / Re: Error converting PWM to PSAM
« Last post by jason on December 21, 2017, 08:40:13 pm »
It works great! Thanks a ton.
17
General Discussion / Re: Error converting PWM to PSAM
« Last post by xiangjun on December 19, 2017, 10:42:12 pm »
Hi Jason,

I've updated the REDUCE Suite to version 2.2.5-2017dec19 in which Convert2PSAM has an additional source option of PFM. An example run on YDR146C (you posted) is shown below:

Code: [Select]
Convert2PSAM -source=pf -inp=$REDUCE_SUITE/data/formats/pfm_YDR146C.dat -psam=stdout
Please have a try, and let me know if you've further problems.

Xiang-Jun
18
General Discussion / Re: Error converting PWM to PSAM
« Last post by jason on December 19, 2017, 02:08:41 pm »
Great! If all it takes is a simple transpose of the PFM matrix, I could handle the rest, but thank you for offering to upgrade the script! Hopefully other users in the future find it helpful.

-Jason
19
General Discussion / Re: Error converting PWM to PSAM
« Last post by xiangjun on December 19, 2017, 01:42:50 pm »
The PFM is row-wise, while the PWM format accepted by Convert2PSAM is column-wise, in order of A, C, G, and T. See $REDUCE_SUITE/data/formats/pwm_ex.dat for an example.

I'll revise Convert2PSAM to accept the PFM format, so you do not need to do extra work.

Xiang-Jun
20
General Discussion / Re: Error converting PWM to PSAM
« Last post by jason on December 19, 2017, 01:27:00 pm »
I see! I don't have much experience with the PWM format, so I thank you for looking into this.

Is the expected PWM format then only integer values, like a count matrix?

Yetfasco also provides the data as a "PFM" or Position Frequency Matrix. In this matrix, all the values are stored as fractions between 0 and 1. http://yetfasco.ccbr.utoronto.ca/1.02/Downloads/Expert_PFMs.tar.gz

The equivalent PFM to YDR146C that you pasted is this:

A       0.403846154     0.653846154     0.0     0.0     1.0     0.0     0.0     0.615384615
T       0.25    0.038461538     0.0     0.0     0.0     0.0     0.0     0.076923077
G       0.25    0.038461538     0.0     0.0     0.0     1.0     0.0     0.076923077
C       0.096153846     0.269230769     1.0     1.0     0.0     0.0     1.0     0.230769231


I also tried converting the PFM to PSAM and got an error, but perhaps I could, for example, scale each PFM to integer values from 0 to 100 and convert that?
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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