Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
Sequence assembly (Read 22077 times)
May 24th, 2010 at 1:02am

Eirik   Offline
YaBB Newbies

Posts: 3
*
 
When using the sequence assembly tool, what format is the reference sequence supposed to be in?

Is the assembly tool meant to be used for assembling a forward and a reverse sequence from Sanger sequencing or is it just for 454 sequences?


Regards

Eirik
 
IP Logged
 
Reply #1 - May 24th, 2010 at 8:10pm

Mikhail Fursov   Offline
YaBB Administrator

Gender: male
Posts: 162
*****
 
Hi!

Quote:
When using the sequence assembly tool, what format is the reference sequence supposed to be in?


The reference sequence could be in any format supported by UGENE. For example: Genbank, EMBL, FASTA, raw sequence..

Short reads file must also be a file with a set of unalignned short-read sequences without gaps, for example FASTA file. UGENE v1.7.0 does not accept alignment format (CLUSTAL, MSF) as the source today.

Extending the set of in/out formats for DNA assembly is one of the goal for the next release.


Quote:
Is the assembly tool meant to be used for assembling a forward and a reverse sequence from Sanger sequencing or is it just for 454 sequences?


Just 454 sequences in this release. Going to cover more functions with the next one. I would suggest using the algorithm from the current version (1.7.0) as a technology preview and send us any issues/usability improvements you have.
 

---
UGENE team
IP Logged
 
Reply #2 - May 26th, 2010 at 12:45am

Eirik   Offline
YaBB Newbies

Posts: 3
*
 
Thanks,

Any plans for extending the assembly to sanger sequences?
 
IP Logged
 
Reply #3 - May 27th, 2010 at 5:51pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Eirik,
further development of dna assembly functionality is very important goal for UGENE team. Currently UGENE allows aligning short reads to reference sequence. Genome aligner plugin uses both forwared and reversed assembling by default.

UGENE supports Fastq data format (Sanger standard). We're planning to include Phred qualities visualization and quality based trimming for aligning in next release. Also we are working on support of Illumina/Solexa data formats.

When speaking about sanger sequencing, do you have any specific data format or sequencer in mind? We are open to suggestions Smiley
 
IP Logged
 
Reply #4 - Jun 4th, 2010 at 4:42am

Eirik   Offline
YaBB Newbies

Posts: 3
*
 
Well, I use an ABI machine, so if it could read those files, it would be great.

Cheers

Eirik
 
IP Logged
 
Reply #5 - Aug 23rd, 2010 at 4:07pm

Myckel Habets   Offline
YaBB Newbies

Posts: 13
*
 
I'm able to open the ABI files on 1.7.2 and see the chromatogram, but is there a way to edit the bases where the calling was not right? (replacing N, deleting extra bases, adding extra bases, etc.)
 
IP Logged
 
Reply #6 - Aug 23rd, 2010 at 6:09pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Editing the bases for ABI files involves sevral steps. Due to format restrictions it is not possible to edit directly the sequence in chromatogram file. First you need to create a new sequence, representing the chromatogram.
It can be done using context menu item "Edit new sequence" in chromatogram viewer.
Check the following documentation pages:
http://ugene.unipro.ru/plugin_chromaview.html
http://ugene.unipro.ru/tutorial_chroma_view.html
or 'Plugins/Chromatogram Viewer' section in the user manual.

There is also a video tutorial available:
http://www.youtube.com/watch?v=9a1wvynLWBo&fmt=18


 
IP Logged
 
Reply #7 - Aug 23rd, 2010 at 9:28pm

Myckel Habets   Offline
YaBB Newbies

Posts: 13
*
 
Ah... thank you. Seems I was clicking on the wrong spot (bottom sequence). One thing though, is it possible to delete or add bases?

And in case of polymorphisms in the sequence you might also want to set R, Y, M, K, S, W, H, B, V and D, maybe something to add for a future version.
 
IP Logged
 
Page Index Toggle Pages: 1