Details
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Type: Bug
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Status: Open
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Priority: Blocker
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: file format issue, na
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Labels:
Description
Import of sequences via stockholm where the end is lower than the start results in Jalview rewriting the sequence limits as start->end as it is shown in the viewer.
Import:
# STOCKHOLM 1.0
#=GF AC RF00005
#=GF SQ 3
#=GF WK Transfer_RNA
X05914.1/238-170 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
X05914.1/400-337 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
//
Results in three sequences with these IDs:
# STOCKHOLM 1.0
X05914.1/238-306 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
X05914.1/400-463 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
//
Import via other formats (e.g. PFAM, by removing stockholm header) results in sequence IDs like:
X05914.1/238-170/1-69 ...
Import:
# STOCKHOLM 1.0
#=GF AC RF00005
#=GF SQ 3
#=GF WK Transfer_RNA
X05914.1/238-170 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
X05914.1/400-337 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
//
Results in three sequences with these IDs:
# STOCKHOLM 1.0
X05914.1/238-306 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
X05914.1/400-463 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
//
Import via other formats (e.g. PFAM, by removing stockholm header) results in sequence IDs like:
X05914.1/238-170/1-69 ...
Attachments
Issue Links
- blocks
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JAL-2861 Non duplicate duplicate sequence when reading in RFAM
- Open