What are the automatic changes conducted by the tool during import?
| Step | ST.25 numeric identifier | Transformation performed by the tool |
1. | 160 | Discard element 160 (number of SEQ ID numbers) |
2. | 170 | Discard element 170 (Software used) |
3. | 210 | Element 210: set sequence identifier. |
4. | n.a. | Set sequence name. |
5. | 211 | Set sequence length |
6. | 212 | Replace molecule type (i) ADN with DNA, (ii) ARN with RNA. |
7. | 212 | Replace molecule type PRT with AA. |
8. | 213 | Replace ‘Artificial Sequence’ and specified equivalents (see UC12, step 5) with ‘synthetic construct’. |
9. | 213 | Replace FR and DE translations of ‘Artificial Sequence’ and specified equivalents (see UC12, step 5) with ‘synthetic construct’. |
10. | 213 | Replace ‘Unknown’ and specified equivalents (see UC12, step 5) with ‘unidentified’. |
11. | 213 | Replace FR and DE translations of ‘Unknown’ and specified equivalents(see UC12, step 5) with ‘unidentified’. |
12. | 221 | Replace obsolete feature key with recommended key (Scenario 8, ST.26, Annex VII) |
13. | 221 | Replace custom feature key with recommended key (Scenario 12, ST.26, Annex VII). |
14. | 221 | Replace VARSPLIC key with VAR_SEQ (Scenario 13, ST.26, Annex VII). |
15. | 221 | Skip transformation of feature key if 1) mol type is PRT and 2) feature key is NOT valid ST.26 and 3) the tool can’t determine whether the location is a single position or a range. |
16. | 222 | Clean location value (remove parentheses, replace invalid separator, reduce redundant ranges,). |
17. | 222 | If negative numbering in PRT sequence, the feature location need to be corrected (Scenario 16, ST.26, Annex VII). |
18. | 222 | Warning that feature location is missing |
19. | 223 | Import 223 after replacing the obsolete feature key with recommended key (Scenario 8, ST.26, Annex VII) |
20. | 223 | Import 223 after replacing custom feature key with recommended key (Scenario 12, ST.26, Annex VII). |
21. | 223 | Import 223 after replacing VARSPLIC key with VAR_SEQ (Scenario 13, ST.26, Annex VII). |
22. | 300-313 | Discard publication information |
23. | 400 | Replace ‘u’ with ‘t’ in RNA sequence. |
24. | 400 | Replace ‘u’ with ‘t’ in DNA sequence. |
25. | 400 | Replace amino acid symbols in 3-letter code with 1-letter code. |
26. | 400 | Warning that the annotation of Xaa symbols must be reviewed |
27. | n.a. | Set skipped indicator to ‘yes’. |
28. | n.a. | Created mandatory source/SOURCE feature for each sequence that: 1) is NOT intentionally skipped and 2) does NOT already have a source feature. |
29. | n.a. | Set value of qualifier /mol_type for ‘synthetic construct’ and protein sequences |
30. | n.a. | Notify the user to set the value of qualifier /mol_type. |
31. | n.a. | Notify the user to set/review the value of the mandatory qualifier |