ACEDB Feature and Group Field Tags
Standard List of Identifiers Dumped by ACEDB (as of August 1999)
rbsk editorial note: This list is 'under construction' and is essentially limited by my incomplete understanding of the ACEDB 'feature map' code written by others in the ACEDB development community...
Note also that GFF dumping for reverse ("UP") strand may be problematic at this time (?)
Feature Field Identifiers
- sequence
- exon
- intron
- CDS
- similarity: sequence homology match (to a database target)
- splice3
- splice5
- atg
- misc_feature
- <assembly_tag>: Value specific to a given tag type
- deletion
- variation
- insertion
- <EMBL feature>: whatever label is stored in the database
- <Clone end>: whatever clone feature name is stored in the database
- ACEDB ?Methods: User defined ?Sequence classification ?Methods
-
fMapSegTypeNames
- MASTER
- CDS_UP
- TRANSCRIPT
- SPLICED_cDNA
- VIRTUAL_SUB_SEQUENCE_TAG
- VIRTUAL_MULTIPLET_TAG
- VIRTUAL_ALIGNED_TAG
- VIRTUAL_PREVIOUS_CONTIG_TAG
- PRIMER
- OLIGO
- OLIGO_PAIR
- TRANS_SEQ
- VISIBLE
- DNA_SEQ
- PEP_SEQ
- ORF
- VIRTUAL_PARENT_SEQUENCE_TAG
- VIRTUAL_CONTIG_TAG
Standard List of Group Tag Identifiers
| Feature | Group Tag | Description |
|---|---|---|
| Sequence | ||
| Exon | ||
| Coding | Sequence | Name of (sub)sequence the feature belongs to |
| Intron | Sequence |
Name of (sub)sequence the feature belongs to
|
| Similarity | Target | Name of target sequence matched by query followed by target sequence interval matched |
| Feature | ||
| Splice_5 | ||
| Splice_3 | ||
| ATG | Note | Value of note is dictName (look->featDict, -seg->parent)??? |
| Assembly_Tag | Note | General details associated with tag |
| Deletion | Allele | Name |
| Variation | Allele | Name |
| Variant | associated data | |
| Insertion | Allele | Name |
| Insert | associated data | |
| <EMBL feature> | Note | associated data |
| <Clone end> | Clone | name |
