Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
how to merge sequences into one (Read 6602 times)
Aug 2nd, 2011 at 6:45am

crAzy pInguin   Offline
YaBB Newbies

Posts: 4
*
 
Just updated UGENE and... All my previous projects are spoiled!

In my projects, I opened genomes from FASTA as merged sequences with 100 Ns between pieces. Now everything is opening as separated sequences and all my documents with whole genome search and HMMER analysis are useless. Tried to re-open FASTA files with genomes - no options to open as merged sequences.

What should I do?
 
IP Logged
 
Reply #1 - Aug 2nd, 2011 at 11:14am

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
*****
 
Hi!
In 1.9.4 we've introduced new "intelligent" mode for opening files. Looks like the option "merge with gaps" was lost. We will fix it ASAP. I've created an issue in the bug tracker: https://ugene.unipro.ru/tracker/browse/UGENE-526

Meanwhile you can do the following.

I've attached a simple Workflow Scenario which allows to read file with multiple genomes and merge them into single FASTA with Ns.
1) Open the attached file merge_with_gaps.uwl in UGENE
2) Set input path (file with your genomes) for "Read Sequence" element. You can do it in the Property editor (See attached screenshot). Make sure that mode is "Merge". You can set the size of a gap between sequences.
3) Set output path for "Write Sequence" element.
4) Click "Run"

After the schema is finished executing, open the result file in UGENE. It will be a merged sequence with exactly 100 Ns between genomes.



 
IP Logged
 
Reply #2 - Aug 2nd, 2011 at 3:32pm

Mikhail Fursov   Offline
YaBB Administrator

Gender: male
Posts: 162
*****
 
Looks like it was me who introduced this regression.

Gonna fix this issue today and provide a link to the snapshot, so you can open your projects again

This fix will also be included into upcoming 1.9.6
 

---
UGENE team
IP Logged
 
Reply #3 - Aug 2nd, 2011 at 8:15pm

Mikhail Fursov   Offline
YaBB Administrator

Gender: male
Posts: 162
*****
 
Fixed. Use any UGENE 1.10 snapshot with revision number >= 976 or wait for 1.9.6 planned to be released in 2 weeks.
http://ugene.unipro.ru/snapshot.html
 

---
UGENE team
IP Logged
 
Reply #4 - Aug 2nd, 2011 at 9:33pm

crAzy pInguin   Offline
YaBB Newbies

Posts: 4
*
 
Thanks a lot Smiley I found the distrib for the old version 1_6 and returned it back, will update in two weeks!
 
IP Logged
 
Reply #5 - Aug 2nd, 2011 at 10:24pm

Mikhail Fursov   Offline
YaBB Administrator

Gender: male
Posts: 162
*****
 
OK.

This regression was introduced by UGENE 1.9.4, so even 1.9.3 must work

To get any old version of UGENE try to download the latest, replace numbers is the URL and download the needed one.
 

---
UGENE team
IP Logged
 
Page Index Toggle Pages: 1