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CharlesEGrant
Sep 28, 2015, 7:00:22 PM9/28/15
to meme-...@googlegroups.com
The MEME Suite provides logograms in two formats: PNG and EPS. PNG is a bitmapped format and generally not suitable for publication. EPS is encapsulated PostScript which is widely used in publications and can be directly imported into LaTex and Word.
To get a publication quality logogram from the MEME web application:
To get a publication quality logogram from the MEME and GLAM2 command-line applications:
The command-line versions of MEME and GLAM2 automatically save EPS versions of the logograms in the output directory. These files can be identified by the ".eps" suffix.
To get a publication quality logogram from the GLAM2 web application:
The GLAM2 HTML output currently only links to the PNG version of the logogram. However, with some work you can get to the EPS version.
Most web browsers will allow you to bring up a context menu by clicking the right button on the mouse.
In Safari or Firefox:
1. Right click on the logogram image
2. The context menu will have menu choices like "View image" or "Open image in new tab". Choose one of those menu items.
3. When the browser displays the image, it will also show the URL for the image in the address bar. The URL for the image will end in the suffix '.png'. In the browser address bar, change the suffix of the URL to '.eps', then hit the "Enter" or "Return" key.
4. This will open the EPS version of the image in the browser, or in a "helper" application. You can then use "Save as ..." from the "File" menu to save a local copy. I've tested this procedure with the Safari and Firefox browsers.
If you are using Internet Explorer 8, the process is a little different:
1. Right click on the logogram image
2. The "Copy link" and "Open link" items will be grayed out. However, you can select "Properties" at the bottom of the menu.
3. A dialog box will open showing various properties of the image. Copy the URL from the field labeled "Address: (URL)". You can then paste the URL into the address bar and change it to the EPS address as above.
Windows doesn't provide a default viewer for the EPS format. When you try to open the EPS URL, the browser may just offer you the option of saving the file.
To get a publication quality logogram from the MEME web application:
- Click on the arrow labeled "Submit/Download" for the logo.
- Select the tab labeled "Download logo"
- Select the download settings for the logogram in the text boxes and list boxes in the tab. EPS is the best format for publication quality logograms.
- Click on the "Download" button.
To get a publication quality logogram from the MEME and GLAM2 command-line applications:
The command-line versions of MEME and GLAM2 automatically save EPS versions of the logograms in the output directory. These files can be identified by the ".eps" suffix.
To get a publication quality logogram from the GLAM2 web application:
The GLAM2 HTML output currently only links to the PNG version of the logogram. However, with some work you can get to the EPS version.
Most web browsers will allow you to bring up a context menu by clicking the right button on the mouse.
In Safari or Firefox:
1. Right click on the logogram image
2. The context menu will have menu choices like "View image" or "Open image in new tab". Choose one of those menu items.
3. When the browser displays the image, it will also show the URL for the image in the address bar. The URL for the image will end in the suffix '.png'. In the browser address bar, change the suffix of the URL to '.eps', then hit the "Enter" or "Return" key.
4. This will open the EPS version of the image in the browser, or in a "helper" application. You can then use "Save as ..." from the "File" menu to save a local copy. I've tested this procedure with the Safari and Firefox browsers.
If you are using Internet Explorer 8, the process is a little different:
1. Right click on the logogram image
2. The "Copy link" and "Open link" items will be grayed out. However, you can select "Properties" at the bottom of the menu.
3. A dialog box will open showing various properties of the image. Copy the URL from the field labeled "Address: (URL)". You can then paste the URL into the address bar and change it to the EPS address as above.
Windows doesn't provide a default viewer for the EPS format. When you try to open the EPS URL, the browser may just offer you the option of saving the file.
Margaret H
Sep 4, 2014, 5:28:13 PM9/4/14
to meme-...@googlegroups.com
Is there a way to get the reverse complement logo from having run TOMTOM in command line?
When you open the TOMTOM html output file the link for the drop-down boxes does not work so I am unable to generate/download an eps for the file in the reverse orientation.
I looked around on ceqlogo as well but could not find a setting to toggle the orientation of the logo
Thanks!
When you open the TOMTOM html output file the link for the drop-down boxes does not work so I am unable to generate/download an eps for the file in the reverse orientation.
I looked around on ceqlogo as well but could not find a setting to toggle the orientation of the logo
Thanks!
James Johnson
Sep 4, 2014, 7:59:19 PM9/4/14
to
Hi Margaret,
The reason the drop down boxes don't work is probably either because you omitted the --with-url option when configuring, or you set it to
which unfortunately (as of 5 September 2014) has not been updated to the latest version of MEME (this is out of our control) and is hence incompatible.
You should be able to get it to work by setting the URL to point to the EBI server with the configure option
.
Using ceqlogo
Assuming I have an IUPAC motif "NTRGGTCAN" which I've generated with the command:
and assuming I want to align it to MA0072.1 from JASPAR_CORE_2014_vertebrates.meme . According to Tomtom these align best at an offset of 5 with both oriented normally so to create the unflipped image I do the following:
Now to flip it we have to reverse complement both motifs and figure out what the shift should be. Now in the example I gave the end of the first motif lines up with the end of the second motif so when we flip it we don't need to apply any shift at all:
The reason the drop down boxes don't work is probably either because you omitted the --with-url option when configuring, or you set it to
You should be able to get it to work by setting the URL to point to the EBI server with the configure option
Using ceqlogo
Assuming I have an IUPAC motif "NTRGGTCAN" which I've generated with the command:
iupac2meme NTRGGTCAN > main.memeceqlogo -o logo.eps -iMA0072.1 JASPAR_CORE_2014.meme -i1 main.meme -s 5
Now to flip it we have to reverse complement both motifs and figure out what the shift should be. Now in the example I gave the end of the first motif lines up with the end of the second motif so when we flip it we don't need to apply any shift at all:
ceqlogo -o logo.eps -iMA0072.1 JASPAR_CORE_2014.meme -r -i1 main.meme -r
CharlesEGrant
Sep 4, 2014, 8:02:35 PM9/4/14
to
Hi Margaret,
The conversion to an EPS file is actually handled by a service on the MEME web site. You have to configure which web site the command line programs will use for services like this with the '--with-url' option to 'configure' before building the MEME Suite command line programs. For example:
./configure --prefix=$HOME/meme --with-url=http://meme.ebi.edu.au/memeh
Once you've re-run 'configure' specifying which MEME Suite server you want to use, you'll need to rerun
make
and
make install
Then you'll need to rerun you TomTom job. The links for generating EPS verisons of the logos should then work.
You can find more details about this in section 2 of the installations guide, "Configuring the Installation".
David Lukac
Nov 24, 2015, 9:49:13 PM11/24/15
to MEME Suite Q&A
If I run a TOMTOM search but the tool does not return any matches, is it possible to generate an eps image from the input motif?
CharlesEGrant
Dec 7, 2015, 8:00:08 PM12/7/15
to MEME Suite Q&A
Hi David,
Did you use MEME to generate the motif file you submitted to TomTom? If so, you should have an EPS file in the MEME output directory, or if you used the MEME web application, you can click on the "Submit/Download" link in the HTML output, and then click on the "Download logo" tab.
If the motif file was not generated using MEME, the MEME Suite doesn't have a web app for generating logograms, but if you are using the command line version you could use the meme2images utility :http://meme-suite.org/doc/meme2images.html distributed as part of the MEME Suite.
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