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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Sequence assembly https://forum.ugene.net/forum/YaBB.pl?num=1274637770 Message started by Eirik on May 24^th, 2010 at 1:02am

Title: Sequence assembly
Post by Eirik on May 24^th, 2010 at 1:02am

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

Title: Re: Sequence assembly
Post by Mikhail Fursov on May 24^th, 2010 at 8:10pm

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.

Title: Re: Sequence assembly
Post by Eirik on May 26^th, 2010 at 12:45am

Thanks,

Any plans for extending the assembly to sanger sequences?

Title: Re: Sequence assembly
Post by Konstantin Okonechnikov on May 27^th, 2010 at 5:51pm

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 :)

Title: Re: Sequence assembly
Post by Eirik on Jun 4^th, 2010 at 4:42am

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

Cheers

Eirik

Title: Re: Sequence assembly
Post by Myckel Habets on Aug 23^rd, 2010 at 4:07pm

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.)

Title: Re: Sequence assembly
Post by Konstantin Okonechnikov on Aug 23^rd, 2010 at 6:09pm

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

ScreenHunter_01_Aug__23_18_06.gif (41 KB | )

Title: Re: Sequence assembly
Post by Myckel Habets on Aug 23^rd, 2010 at 9:28pm

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.