WormBase Model:Homol info

WormBase Models

Model

#Homol_info Align Int UNIQUE Int UNIQUE Int
                        // not needed if full alignment is ungapped
                        // one row per ungapped alignment section
                        // first int is position in query, second in target
                        // third int is length - only necessary when gaps in both sequences align
            AlignDNAPep Int UNIQUE Int UNIQUE Int
            AlignPepDNA Int UNIQUE Int UNIQUE Int
            Target_species UNIQUE ?Species
            EMBL_dump UNIQUE EMBL_dump_YES
                             EMBL_dump_NO
                        // overrides for embl dump based on method
            EMBL_qualifier Text
                        // additional to those in the method, includes '/'

Proposed Changes

#Homol_info Align       Int UNIQUE Int UNIQUE Int
            Target_species UNIQUE ?Species 
            AlignDNAPep Int UNIQUE Int UNIQUE Int
            AlignPepDNA Int UNIQUE Int UNIQUE Int
            Match_string UNIQUE RefFwd_HitFwd UNIQUE Text
                                RefFwd_HitRev UNIQUE Text
                                RefRev_HitFwd UNIQUE Text
                                RefRev_HitRev UNIQUE Text

Basically get rid of the EMBL tags, and add support for cigar strings.

unused tags

• EMBL_dump
• EMBL_qualifier