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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 
PlatformPCOSWindows 
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
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.
TagsNo tags attached.
Attach Tags (Separate by ",")
First NameChih-Ting
Last NameHsu
Emailcthsu110311@gmail.com
Confirm Emailcthsu110311@gmail.com
Attached Files? file icon Final_MSA_Shark_Paper_MEGA.meg (63,075 bytes) 1969-12-31 17:33
png file icon 圖片_2022-05-15_160949490.png (32,789 bytes) 2022-05-15 01:17

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-  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 (reporter)
2022-12-05 07:00

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(0006437)
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2023-04-14 18:34

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- Issue History
Date Modified Username Field Change
1969-12-31 17:33 user614 Note Added: 0002441
1969-12-31 17:33 user614 Status new => resolved
1969-12-31 17:33 user614 Resolution open => no change required
1969-12-31 17:33 user614 Assigned To => user614
1969-12-31 17:33 user614 Tag Attached: parsing_error
2022-05-15 01:17 guest New Issue
2022-05-15 01:17 guest File Added: 圖片_2022-05-15_160949490.png
2022-12-05 07:00 guest Note Added: 0005906
2023-04-14 18:34 guest Note Added: 0006437


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