MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0003680MEGASequence Data Explorerpublic2022-05-15 01:172023-04-14 18:34
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSWindowsOS Version10
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameChih-Ting
Last NameHsu
Emailcthsu110311@gmail.com
Confirm Emailcthsu110311@gmail.com
Summary0003680: Wrong codon start in Sequence Data Explorer
DescriptionIn Sequence Data Explorer, when you select 3rd site as codon start in "Genes/Domain organization" the codon start will actually be set to 2nd codon, and when select 2nd site, it would be 3rd actually.
Steps To Reproduce1. Open any aligned MSA with protein-coding DNA.
2. Open it in Sequence Data Explorer
3. "Data" -> "Select and Edit Genes/& Domain...
4. "Edit" -> "Is Coding Codon Start" -> Select the "3rd Site"
5. The codon start would be actually 2nd site in Explorer.
Additional Information
TagsNo tags attached.
Relationships
Attached Files? Final_MSA_Shark_Paper_MEGA.meg (63,075) 1969-12-31 17:33
https://megasoftware.net/mantis_bt/
png 圖片_2022-05-15_160949490.png (32,789) 2022-05-15 01:17
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user614Note Added: 0002441
1969-12-31 17:33user614Statusnew => resolved
1969-12-31 17:33user614Resolutionopen => no change required
1969-12-31 17:33user614Assigned To => user614
1969-12-31 17:33user614Tag Attached: parsing_error
2022-05-15 01:17guestNew Issue
2022-05-15 01:17guestFile Added: 圖片_2022-05-15_160949490.png
2022-12-05 07:00guestNote Added: 0005906
2023-04-14 18:34guestNote Added: 0006437

Notes
(0002441)
user614   
1969-12-31 17:33   
Hello Tiffany,
I am responding to the question you had regarding an error message when opening an alignment file in MEGA. The error is caused because the alignment file is not formatted according to the .meg file specification. First, the first two sequences have the same name so MEGA is trying to read it as if the sequence data was interleaved. Second, the .meg specification requires that all sequences in the alignment are the same length but that is not the case. The easiest way to fix this is probably to use MEGA to create the sequence alignment from a FASTA file. Then you can save the alignment in the .meg format and everything should be correct.

Best regards,

Glen Stecher
(0005906)
guest   
2022-12-05 07:00   
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(0006437)
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2023-04-14 18:34   
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