UGENE Forum - Digest into fragments

Nov 1^st, 2011 at 11:48pm

JohnR Offline
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Posts: 17

The "Digest into Fragments" and "Molecular Cloning in Silico" options are great! It would be helpful if the display on "Digest into Fragments" gave the size of the fragment, and if there were a table option to show sizes of all fragments after digesting with particular enzyme(s). Although the current display (attached) gives the location of fragment ends, if you have more than a couple of fragments, doing the subtraction for all of them is a bit tedious. I looked in the user manual and didn't see these options. Thanks!

UGeneFragmentDisplay.jpg (31 KB | )

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Reply #1 - Nov 3^rd, 2011 at 5:19am

Konstantin Okonechnikov Offline
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Posts: 173

John, could you please describe what kind of "table option" do you mean?

So far there is only a read-only list of created fragments available as a report after digestion (see attached screenshot). I suppose the size of a fragment could be added as annotation to the fragment.

The table of all created fragments is also avaialble in "Clonning->Construct molecule" dialog.

screenshot_clonning.gif (52 KB | )

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Reply #2 - Nov 8^th, 2011 at 10:29pm

JohnR Offline
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Posts: 17

That kind of table was exactly what I was looking for. I just missed the button in the lower right corner for "notifications" to see the results in tabular form. It might be helpful to other users to add something about this option for the report and how to get to it in the users manual when it is next revised.

Again, thanks for all the work you do in continuing to update and improve UGene. I use it both for research and for students in an undergraduate molecular biology class.

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Reply #3 - Nov 8^th, 2011 at 10:59pm

JohnR Offline
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Posts: 17

I just looked at the table of fragments more carefully, and noticed odd results. I don't know if this is because I didn't have use the correct settings in the "Digest into Fragments" dialogue, or if there is a glitch with digesting circular fragments. Input DNA is a circular DNA with Pst I sites at 995 and 3414. The map generated when I ask for the location of the Pst I sites is correct. However, the "Digest into Fragments" task report shows two fragments, 2416 and 3048, rather than the correct sizes of 2416 and 4045. This is because fragment 2 stopped at 0/6461 rather than continuing around the circular DNA to the next Pst I site. At first I wondered if I had accidentally indicated that the DNA was linear, but the report clearly shows (circular). The map, "Digest into Fragments" task report, and a report generated by New England Biolabs NEBCutter are attached. I could send along the sequence file also, if that would help.

UGene_FragmentDigest.doc (170 KB | )

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Reply #4 - Nov 10^th, 2011 at 6:05am

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Quote:

That kind of table was exactly what I was looking for. I just missed the button in the lower right corner for "notifications" to see the results in tabular form. It might be helpful to other users to add something about this option for the report and how to get to it in the users manual when it is next revised.

Good suggestion! The manual is not updated as frequently as it should be. I hope we will include information about notifications with the next release.

Quote:

Again, thanks for all the work you do in continuing to update and improve UGene. I use it both for research and for students in an undergraduate molecular biology class.

Thanks for your kind words! UGENE is getting better thanks to users' reports and feedback

Quote:

Input DNA is a circular DNA with Pst I sites at 995 and 3414. The map generated when I ask for the location of the Pst I sites is correct. However, the "Digest into Fragments" task report shows two fragments, 2416 and 3048, rather than the correct sizes of 2416 and 4045. This is because fragment 2 stopped at 0/6461 rather than continuing around the circular DNA to the next Pst I site.

Yep, it's a bug, it will be fixed ASAP:
https://ugene.unipro.ru/tracker/browse/UGENE-696

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Reply #5 - Dec 22^nd, 2011 at 4:46pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Bug fixed! Available soon from latest snapshot and also will be included in upcoming 10.0.1.

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