When I input a FASTA background, after it converts to aligned sequences of the proper width, will it remove sequences from this background that are identical to the input foreground sequences?
No, currently foreground sequences are not removed from the background. However, this is a feature we plan to add in the near future.
If I want to upload my own background, do I have to upload aligned sequences that are the same width of the foreground?
You can input a FASTA background and the tool will automatically convert it to aligned sequences of the proper width.
My pLogo is taking a long time to generate, is the web site broken?
The pLogo computational tool utilizes cached backgrounds to increase the speed of pLogo generation. If you are making a pLogo with a width that is not in the cache, the computation will take significantly
longer than usual. However, subsequent pLogos at that width (and for the same background data set) should be generated much quicker. (NOTE: this only applies to background data sets provided on the web site, user
uploaded backgrounds are not cached and thus will typically take longer for pLogo generation).
What are the benefits of creating a user account?
All pLogos generated while logged into your user account will be saved in your private job history. Having an account allows you to search through your job history, retain all foreground and background
data sets, and allows you to optionally send job URLs to colleagues. It also gives you the ability to mark jobs as "favorites", allowing you to quickly return to an important job in the future.
I received the error "Unable to create new image" when trying to export my pLogo. What went wrong?
Our pLogo image generation algorithm currently does not support DPI above 300 or a height above 1100px. We recommend using a 2:1 aspect ratio for all exports and a DPI of 300 for images being used in print.
Can I use tryptic peptides from mass spectrometry as a foreground input in pLogo?
No, pLogo only supports fixed-width aligned foregrounds. However, you can use our peptide extender utility at http://schwartzlab.uconn.edu/pepextend/ to generate aligned foregrounds from your peptide data set.
Why do some pLogos automatically have an initial position fixed while others do not?
The pLogo web site will automatically set the initial fixed position to the most conserved residue above the threshold of 0.80 - if no residues are above the 0.80 conservation threshold, the pLogo will be generated
with no initial fixed positions.
Not all of the foreground sequences I input were used for pLogo generation - what happened?
Foregrounds and preprocessed and filtered before being used for pLogo generation. Sequences with invalid characters or widths that do not match the majority will be discarded by this preprocessing step. The foreground
preprocessing will also remove duplicate sequences in the foreground (retaining only 1 instance of the duplicated sequence). To see which sequences were removed by the foreground preprocessing stage, click the
"foreground preprocessing" tab below the foreground input box. Numbers in the right hand column of this window can be clicked to view the sequences that were removed for a given reason.
How can I see the probability values used to generate the pLogo image?
You can export the position weight matrix (PWM) used to generate any pLogo image by clicking the "export" tab on the left side of the image. In the export window, click "Export raw position weight matrix values" to download
a text file containing the PWM.