General Category >> Help and How-to >> Problem running alignments

Message started by Covux on Feb 15th, 2013 at 8:02am

Title: Problem running alignments
Post by Covux on Feb 15th, 2013 at 8:02am

I have been using Ugene for the first time today,
After watching some videos and reading the manual i got started to make an aligment with some DNA sequences of a bacteria.

I have 15 DNA sequencies whiche are all around 4.4M Nucleotides.
I have been able to align them in an .aln file.

When i want to alignmen them using Kalign or ClustalW they are able to start. i don't get an error when i want to align them.

How ever they keep stuck at 14%(when using Cluster) and 75%(when uding Kalign). When i use less sequences i keep getting the same results.

I am using W7 64 Bit and i am using the 64 bit full version of the program.

I have 8GB of RAM and have appointed 6GB to the program.
Increasing or decreasing doesn't influence the result.

When i run the program it doesn't consume more then 2GB of my RAM and the activity of my CPU cores(have 4) are all around 80-90%.

Another thing is that when i start the alignment they get at 14% and 75% really quick and then remain stuck there for a few hours( 2 hours when i am typing this).

I hope you guys can give me any advice for helping this issue.


Title: Re: Problem running alignments
Post by Yuriy Vaskin on Feb 15th, 2013 at 2:05pm
Hello, Covux!

Thanks for your question. BTW I believe our video tutorials and documentations gave you enough information to get started with UGENE.

In multiple alignments we rely on external algorithms like ClustalW, Kalign, MUSCLE, etc. Unfortunately they are not designed to align long sequences like bacterial genomes. You could try Mauve or Mummer for that purpose. We've already planned to integrate one of that algorithms.

Title: Re: Problem running alignments
Post by Covux on Feb 15th, 2013 at 2:27pm

Thank you for your answer i'll look into those programs.

Will one of those programs be integrated in the verison that will be releases this month?

I have a other question:

is it somehow possilbe to look for STR in more then 1 aligment at the time.

When i have one sequence i can look for STR, but i want to look for STR in more then one aligment so i can sport diffrences in length very fast.
Is this possible?


Title: Re: Problem running alignments
Post by Yuriy Vaskin on Feb 18th, 2013 at 12:09pm

our Alignment Editor doesn't support annotations yet. But Sequence View does. You can add several sequences on one Sequence View ( and find STR in all the sequences. This makes the spotting of differences posible. It might be convenient to lock scrolls of the sequences (

Integrating tools for whole genome alignment is not a plan for the coming versions ( We're focused on Multiple Alignment Editor (Variations highlighting, pairwise alignment, clustering) and NGS pipelines.

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