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
  • 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
* quick link - http://q.sanger.ac.uk/s3fox8fl