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
      

	                    
Confirmed_by_EST
	                    
Confirmed_by_cDNA
	                    
Confirmed_by_homology
	                    
Confirmed_in_UTR
      

   
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