[UGENE-6136] Problem finding a primer when characters insertion is required at the beginning of the primer Created: 29/Jun/18  Updated: 19/Feb/20  Resolved: 19/Feb/20

Status: Closed
Project: UGENE
Component/s: Basic-Nucl
Affects Version/s: 1.30
Fix Version/s: 1.31

Type: Bug Priority: Blocker
Reporter: Dmitrii Sukhomlinov Assignee: Dmitrii Sukhomlinov
Resolution: Fixed  
Labels: request
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Attachments: PNG File extended.png     PNG File not_extended.png     File ugene_sequences.tar.gz    
Story Points: 3
Assigned Tester: Svetlana Samoilenko
Sprint: DEV-31-4, DEV-31-5, DEV-31-6-RELEASE
Affect Type: Userdefined

 Description   

See the attached archive. There are two sequences and one file with forward and reverse primers. The second (extended) sequence has additional 12 'T' characters at the beggining.

Scenario:

  1. Open a sequence.
  2. Open the "In Silico PCR" tab on the options panel.
  3. Input the forward and reverse primers from the third file.
  4. Set the number of mismatches for the forward primer to "27" (note that it is enough to set the value to "22" for the extended sequence).
  5. Click "Find product(s) anyway".
    Current result: A product is found only in case of the extended sequence.
    Expected result: The product is found in both cases.

In the attached pictures you can see that in case of "not_extended" sequence the primers searching algorithm needs to insert additional gaps at the beginning of the sequence, but it doesn't do that. In case of "extended" sequence, the beginning is already filled with 'T' chars, so the algorithm can find the place correctly.

This issue was created according the following issue on GitHub:
https://github.com/ugeneunipro/ugene/issues/38



 Comments   
Comment by Dmitrii Sukhomlinov [ 19/Jul/18 ]

Previously, the number of mismatches was calculated as a minimum of values:

  • "Mismatches", specified on the "In Silico PCR" tab of the options panel
  • A half of the primer length

This has been modified as follows: there may be any number of mismatches, but they are searched for in the 5' part of the primer, i.e. "the primer length - 3' perfect match".

Comment by Aleksey Tiunov [X] (Inactive) [ 01/Aug/18 ]

Something is wrong.

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