[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 |
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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: | extended.png not_extended.png 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:
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: |
Comments |
Comment by Dmitrii Sukhomlinov [ 19/Jul/18 ] |
Previously, the number of mismatches was calculated as a minimum of values:
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. |