User Questions
Post any questions here to see if anyone else out there might be able to answer
Please add questions to the bottom of the page.
Don't delete anything from the page.
Thanks.


Hi,
I'm trying to troubleshoot and design some rules for various Tm calculators. What is the formula for Tm calculation in ApE? Is there a table of thermodynamic parameters and/or assumptions which determine the calculation?
Thanks.
I use dS and dH values from SantaLucia J., Proc. Nat. Acad. Sci. 95: 1460-1465 (1998), with salt correction from SantaLucia, J., Jr., Allawi, H. T., and Seneviratne, P. A. (1996).

What salt concentration do you assume?
Salt and oligo concentration can be set by the user in the primer find dialog.


Hi, do you think it would be possible to add the Codon usage in C. elegans in the help section?
here is a link
http://www.ncbi.nlm.nih.gov/books/NBK20194/table/A5923/?report=objectonly

Thanks!


ApE install / use on a Ubuntu system ?

Hi,
are there easy ways to use ApE on a Ubuntu system, does anyone have experience with it ?
- at the level of a script ? (what procedure to do this?)
- at the level of Wine emulation ?
- at the level of free win emulators ?
Thanks!


Hi. I was wondering what the blocks, mismatch penalty, N-W max, gap penalty and gap ext. penalty mean in the align two sequences feature? Thanks!
  • Blocks is the block size for the heuristic block align function- the routine tries to align blocks of identity first, then does a base-by-base alignment using Needleman-Wunsch. N-W is slow and for longer sequences too slow, which is why it tries to align blocks first. Gap penalty and gap extension penalty are the scoring penalties for the affine scoring- there is a penalty for opening a gap and a penalty for extending a gap.

Hi!
I was wondering if .png format support could be added for future versions, particularly for viewer export. I'm having problems using .svg as some browsers (and the Wiki servers) interpret it as an "old" version and don't render it correctly. By the way, EXCELLENT program. Kudos!
H├ęctor
  • Possible, but only as a screen shot- if there are overlapping windows, they will be included in the shot.
  • I'd rather stick with vector formats- do you have any details on the problems with the svg- which are offending commands, or which browsers don't render corectly?



Hi!
I was wondering if it is possible to "splice-translate" a sequence. One can define regions as introns, and I was wondering if the ApE "translate" tool could translate only the exons of a sequence using this information.
Thanks!

PS: Btw, as this is my first post, just wanted to say: amazing software - I recommended it in my lab, and now everyone is using it :)
  • The text map function does this- if you turn on features, cds features are translated
  • I'm going to add the option of making a new sequence out of a feature, splicing out gaps.




Hi again,
I was thinking that it might be a good idea if features could be organised according to the length of the sequence anotated, so that for example, primers would always be above exons and exons above genomic regions of genes....
Is it something easily doable?
Thanks

Hi,
I was wondering if it would be possible to add the repeat finder tool to ape?
http://tandem.bu.edu/cgi-bin/trf/trf.300.pl
Thanks
Pablo
  • It should be possible to add this tool in a similar way to the way NCBI BLAST is done. I'll need to look into whether they allow outside links.


Hi,
Woudl it be possible to be able to visualise primer dimers (homo/hetero) and hairpins easily?
Thanks
Pablo
  • Right- I want to add that to the primer window.



Hi,
in the find tool, would it be possible to have a "find" option in addition to "find next" and "find prev"? I think it's good to be able to search on one go the whole sequence, independently of the direction...
Would it also be possible, to have a "find all" option. I am looking for primers in a region full of repeats and it would be nice to be able to quickly check if the primers are repeated as well...
Thanks
Pablo
  • Look at the latest alphas (2.0.33 for example). There is now a wrap option in the find dialog.


Hi, I was wondering if it would be possible to get figures as the one here :
http://scienceblogs.com/pharyngula/upload/2006/09/cat_tas1r2_struc.gif
straight from ape?
I think I remember it is possible when using a genebank format for a gene, but I couldn't manage to get the same from the feature annotation...
I think a software that does that is Gene Palette...?
Thanks a lot!!!!
Pablo
  • This will be coming soon- I've got most of it working in circular maps- you can edit the width, and the arrows (fwd and reverse). If a sequence is short (like a mutation) you can make an arrow that points towards the baseline. It will be working in linear maps in short order.

Hi, I was wondering how to align two DNA sequences while viewing their translations? For instance, there may be a nucleotide difference between two sequences but it could be a silent mutation. Thanks!!


Hi. When I make a graphical map, overlapping features mask each other. Is there a way to have overlapping features show up on different lines? Thanks!




Hi, Is there any way to align multiple sequences? So far, I've managed to align two at a time. Thanks in advance!
  • Yes, download version 2.0.25 from the alphas download site. The alignment routine has bee completely rewritten, and now you can align multiple sequences or abi files to a reference.
So cool!! Thank you!!----

Is there a way to add personal notes or comments to a sequence? For example, I have a sequence for a plasmid and want to list all the articles that talk about that plasmid. Thank you for your help!
  • Yes, click on the little icon on the lower right of the sequence. That will open the file comment box where you can type or paste in as much text as you like. In preferences, you can make the comment box open by default, and can set the default size of the box.
Fantastic, thank you so much! I completely just didn't see that pencil/notepad icon.


I was interested in the multiple sequence alignment feature available in newer versions of ApE so I downloaded the v2.0.29 for linux. However, when I start the program, it asks for Accessory Files folder. If I use the one that comes with current version, alignment routine does not seem to work. Help! Thank you.


RE: the Feature Libraries
Can you tell me what the last two columns are for? (They are typically filled with zeros.)

Thanks. CR.
  • Those are reserved for future use. They will probably be used for formatting the display of features in the new update that I'm working on- you'll be able to set the width, arrow type, height above the line, etc.

Hi,
is there a paper about ApE which I can use for citation?
Thanks!
DD
  • Not at this time. Thanks for thinking of it though.


Hi,

The webpage states that 2.0.37 is the latest version of APE. However, when I downloaded the current version for OS X, I only got 2.0.36. Where can I get the latest version for Mac OS X? Thanks.
  • Sorry, the website wasn't clear- I think I changed it to be more clear now.
  • Version 2.0.x has been promoted from alpha to the release branch. Latest releases are now found by clicking on the icons at the top of the web page. The latest alphas directory is going to be inactive until a new alpha branch is started.

Got you. But the os x current version was made from May 30th. The latest alpha was from July 12th. If the alpha is the release branch now, shouldn't the os x current version also be made from July 12th?
  • Ok, I think it's fixed now. v2.0.37 should be the current version on Win and OSX links

I think your link of the OSX is biologylabs.utah.edu/jorgensen/wayned/ape/Download/Ape_OSX_current.dmg,
but it should be biologylabs.utah.edu/jorgensen/wayned/ape/Download/Mac/ApE_OSX_current.dmg.
  • Looks good on my end- try reloading the page to clear any cached copies of the page.


Hi

I wrote a python script that searches for my primers in an ApE file and then adds them in as features by writing to the .ape file as text. (It works really well- thanks for making the ApE files so easy to edit in a text editor).

My question is related to the one about sorting features by size. I want the primers to appear above any other features. What governs the order of appearance? I tried adding the primer features above the old ones in the ApE file but that doesn't seem to do it. Where is the data about order of appearance stored?

Thanks
  • The last feature in the features list should be the top-most, while the first should be bottom-most.

Thank you

I'd like to cite ApE in the publication I am working on right now. Unfortunately, I was unable to find information on how to cite your program.

Thank you!
  • You can cite it as a personal communication from me. email me if you have any specific questions.


Hi all,
I was wondering if there's any way to adjust ApE to retina display, please.

Also, thanks for developing such an awesome software.
  • Is it just the icons that don't look good? What parts of the interface need the most work on a retina display- I've never seen ApE on a retina display.

Thanks for the reply. It's the icons and the fonts. It's becoming very disturbing to read a sequence when everything is out of focus.
  • Since I don't have a retina display- can you email me at wdavis@biology.utah.edu and I can send you some new code to test?

Absolutely. Thanks a lot for your time. I do really appreciate it.


Hi,
I just downloaded the new version of ApE on my new computer (with Windows 8) and I can view my old saved files of ApE, but when I open a new DNA file I can't paste any new sequences into it. I can type new sequences, but not copy-paste them in. Has anyone else had this problem?
Thanks!

  • I haven't heard of this issue from others running Windows 8. Are you running as administrator? There might be some form of security setting blocking copy paste functions. Do you have any num-lock or function lock or other modifiers of keystrokes pressed? Those might be causing the Ctrl-C and Ctrl-V to be sent as a different key set. Do other keyboard shortcuts work? Does copy-paset work from the menu items?

I'm not sure if I am running as administrator, how would I check this? I've checked my num-lock, but have tried Ctrl-V and using the copy-paste from the menu items...nothing works. I've also tried older versions, but nothing seems to work.
  • To run as administrator, right click on the icon, click "Run as administrator". Since the menu option doesn't work, it may be a security issue. Another thing to try would be press ctrl-0 (zero). There should be a terminal window that pops up. In there, type clip_paste $w. See if any error happens. If no error, type clip_cut_copy $w, then type
    clip_paste $w. Let me know what happens.
Ok, I clicked "Run as administrator" and even restarted my computer, but that didn't work. Then I got the terminal window and typed clip_paste $w - no error occurred, so I typed in the clip_cut_copy $w, then clip_paste $w - nothing happened and it still won't let me paste. I do have past ApE files on my computer, that I transferred from my other computer and I can take those sequences and copy and paste them into new DNA windows, and I can type in new sequences, I just can't paste any new sequences into a new, or old window, regardless of the format that the sequence is in. Any other suggestions? I appreciate the help! Thanks!
  • Copy and paste between ApE windows works, so the copy paste mechanism is basically intact. Just copy and paste from an external source is broken. It might be a formatting issue. Can you paste the same content into notepad? Can you copy from Notepad and paste into ApE?

No, I've tried word and notepad and I can't copy and paste anything from those programs into ApE. Even if I just type AGT in word and try to paste it in, it doesn't work. If I type AGT into ApE I can copy and paste it into word or back into the same ApE file, I just can't paste a new file....
  • So you can copy and paste between ApE windows and from an ApE window into notepad, and if you paste into notepad you can paste back into ApE, but if you type in Notepad, you can't paste back into ApE? The workaround would be to save the external text as a Fasta file (put a line with ">" as the first character) then you can open that with ApE. Do you have something running that accelerates copy and paste events, or adds extra shortcuts? That can confuse the copy/paste between applications. Do you have a non-English keyboard option installed? I'm not sure what else to say- it's working in all ways except from external programs and that can be worked around. No other user has reported this issue, so I'm not sure how to proceed.
  • you might look here: http://answers.microsoft.com/en-us/windows/forum/windows_8-files/copy-and-paste-feature-not-working-in-windows-8/22fe8b55-e1ab-48f1-a413-722f9ca108c1
Thanks, saving it as a FASTA file worked! I appreciate your help!

Hello, I have exactly same problem as above: "Copy and Paste" doesn't work.

Sequence from Word/ Internet Browser/ Notepad (Copy)-> Ape program(Paste) doesn't work.
So,
1.ApE(Copy)->ApE(Paste) :Works
2.ApE(Copy)->Word/Notepad(Paste): Works
3.Notepad(Copy)->ApE(Paste) :Doesn't work
4.Writing with keyboard in ApE: Works
2->3 doesn't work either

I am not sure this is problem of Windows 8 or general system, because I don't have this issue in any other programs. I don't get what means exactly by "Saving it as a FASTA file" I tried ">atagg" and copy but it didn't work either. Let me know if there is a solution for this. I appreciate your efforts!!
___

Hi,
The fact that graphic svg files saved from ApE (version 2.x) are not readable by browsers (I tried Firefox and IE; windows PC) was already mentioned above. They also won't open in the svg drawing program Inkscape. I would add that svg files from version 1.x ARE compatible with these applications.

Any chance you could restore svg compatibility?

Thanks for making your program available!

  • Sorry- a bug in version 2.0.47 broke the svg export. If you edit the svg file in a text editor you can fix the svg file to be read anywhere. Edit it so that the first line of the file looks like:<svg width="704px" height="392px" xmlns="http://www.w3.org/2000/svg" version="1.1" preserveAspectRatio="xMidYMid meet" viewBox="-339 -205 704 392">. You should just need to move a > character. The bug has been fixed in the development code and will be rolled out sometime soon, probably after Tcl/Tk fixes some of the known outstanding issues with Mavericks compatibility.

Thanks much for the workaround information--seems to work.


Hello,
I'm an avid ApE user in my undergrad research program as well as upper level coursework. Recently I've run into issues with ApE not being compatible with Chromebooks and Mac OS X El Capitan. It doesn't seem to run at all on Chromebooks and is very sluggish with El Capitan. Is there an easy fix or an impending update for dealing with these issues?
Thanks!

As far as the Chromebook issue. It should be able to run ApE the same way that other Linuxes do. You'll need to get Linux running, though. Otherwise, no, just like most software, it won't run on a chromebook. It's possible that in the future, I could get it working there.

I'm looking into the El Capitan issues.


Hello,
Thanks for APE - essential for our work. I've been using APE (version unknown) for many years on an old MacbookPro (OS 10.6.8) and have lots of valuable annotated files. I've recently updated to new MacbookPro (macOS Sierra 10.12.3) and installed latest APE release (v2.0.51). It's working (which is great) but I've found a few issues:
- "Edit Features" is missing from Features menu (crucial to correct and remove features)
- Toolbar text/menus are sharp on Retina Display, but text in open windows/files are slightly blurred (readable and workable, but hard on eyes after awhile...)
- When using "Find" function in .abi files, corresponding peaks/bases are highlighted, but with a one peak/base offset (workable, but odd).
If useful, I have screenshots of these problems that I can send along.
I've tried some older releases of APE on new computer (2.0.47, 2.0.37?). Older versions do not have the "fuzzy text" problem, the "Edit Features" is back, but suffer from more serious hangs and some black boxes, and are generally not workable.
Constant system updates must be headache for you, but if you have any advice to help on these topics, we'll be grateful... Thanks!

Hi,
Actually, I took out the edit features dialog because it's now much easier to edit features using the features list at the top of the window (right click on any of the properties to edit them), or by right-clicking on the feature in the sequence and selecting Edit feature, Hide Feature, or Delete Feature.

Not sure what I can do about the sequence text blurring- maybe try changing the font that you are using for sequences? I haven't heard this bug on the latest release before.

I'll look into the off-by-one bug in the abi find.

The older versions are definitely going to have non-workable bugs on a newer system.