<!-- ============================================
     ::DATATOOL:: Generated from "seq.asn"
     ::DATATOOL:: by application DATATOOL version 2.4.4
     ::DATATOOL:: on 09/25/2012 23:04:47
     ============================================ -->

<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-Sequence"
================================================= -->

<!--
$Revision: 375986 $
**********************************************************************

  NCBI Sequence elements
  by James Ostell, 1990
  Version 3.0 - June 1994

**********************************************************************
-->

<!-- Elements used by other modules:
          Annotdesc,
          Annot-descr,
          Bioseq,
          GIBB-mol,
          Heterogen,
          MolInfo,
          Numbering,
          Pubdesc,
          Seq-annot,
          Seq-data,
          Seqdesc,
          Seq-descr,
          Seq-ext,
          Seq-hist,
          Seq-inst,
          Seq-literal,
          Seqdesc,
          Delta-ext,
          Seq-gap -->

<!-- Elements referenced from other modules:
          Date,
          Int-fuzz,
          Dbtag,
          Object-id,
          User-object FROM NCBI-General,
          Seq-align FROM NCBI-Seqalign,
          Seq-feat,
          ModelEvidenceSupport FROM NCBI-Seqfeat,
          Seq-graph FROM NCBI-Seqres,
          Pub-equiv FROM NCBI-Pub,
          Org-ref FROM NCBI-Organism,
          BioSource FROM NCBI-BioSource,
          Seq-id,
          Seq-loc FROM NCBI-Seqloc,
          GB-block FROM GenBank-General,
          PIR-block FROM PIR-General,
          EMBL-block FROM EMBL-General,
          SP-block FROM SP-General,
          PRF-block FROM PRF-General,
          PDB-block FROM PDB-General,
          Seq-table FROM NCBI-SeqTable -->
<!-- ============================================ -->

<!--
*** Sequence ********************************
*
-->
<!ELEMENT Bioseq (
        Bioseq_id, 
        Bioseq_descr?, 
        Bioseq_inst, 
        Bioseq_annot?)>

<!-- equivalent identifiers -->
<!ELEMENT Bioseq_id (Seq-id*)>

<!-- descriptors -->
<!ELEMENT Bioseq_descr (Seq-descr)>

<!-- the sequence data -->
<!ELEMENT Bioseq_inst (Seq-inst)>

<!ELEMENT Bioseq_annot (Seq-annot*)>

<!--
*** Descriptors *****************************
*
-->
<!ELEMENT Seq-descr (Seqdesc*)>


<!ELEMENT Seqdesc (
        Seqdesc_mol-type | 
        Seqdesc_modif | 
        Seqdesc_method | 
        Seqdesc_name | 
        Seqdesc_title | 
        Seqdesc_org | 
        Seqdesc_comment | 
        Seqdesc_num | 
        Seqdesc_maploc | 
        Seqdesc_pir | 
        Seqdesc_genbank | 
        Seqdesc_pub | 
        Seqdesc_region | 
        Seqdesc_user | 
        Seqdesc_sp | 
        Seqdesc_dbxref | 
        Seqdesc_embl | 
        Seqdesc_create-date | 
        Seqdesc_update-date | 
        Seqdesc_prf | 
        Seqdesc_pdb | 
        Seqdesc_het | 
        Seqdesc_source | 
        Seqdesc_molinfo | 
        Seqdesc_modelev)>

<!-- type of molecule -->
<!ELEMENT Seqdesc_mol-type (GIBB-mol)>

<!-- modifiers -->
<!ELEMENT Seqdesc_modif (GIBB-mod*)>

<!-- sequencing method -->
<!ELEMENT Seqdesc_method (GIBB-method)>

<!-- a name for this sequence -->
<!ELEMENT Seqdesc_name (#PCDATA)>

<!-- a title for this sequence -->
<!ELEMENT Seqdesc_title (#PCDATA)>

<!-- if all from one organism -->
<!ELEMENT Seqdesc_org (Org-ref)>

<!-- a more extensive comment -->
<!ELEMENT Seqdesc_comment (#PCDATA)>

<!-- a numbering system -->
<!ELEMENT Seqdesc_num (Numbering)>

<!-- map location of this sequence -->
<!ELEMENT Seqdesc_maploc (Dbtag)>

<!-- PIR specific info -->
<!ELEMENT Seqdesc_pir (PIR-block)>

<!-- GenBank specific info -->
<!ELEMENT Seqdesc_genbank (GB-block)>

<!-- a reference to the publication -->
<!ELEMENT Seqdesc_pub (Pubdesc)>

<!-- overall region (globin locus) -->
<!ELEMENT Seqdesc_region (#PCDATA)>

<!-- user defined object -->
<!ELEMENT Seqdesc_user (User-object)>

<!-- SWISSPROT specific info -->
<!ELEMENT Seqdesc_sp (SP-block)>

<!-- xref to other databases -->
<!ELEMENT Seqdesc_dbxref (Dbtag)>

<!-- EMBL specific information -->
<!ELEMENT Seqdesc_embl (EMBL-block)>

<!-- date entry first created/released -->
<!ELEMENT Seqdesc_create-date (Date)>

<!-- date of last update -->
<!ELEMENT Seqdesc_update-date (Date)>

<!-- PRF specific information -->
<!ELEMENT Seqdesc_prf (PRF-block)>

<!-- PDB specific information -->
<!ELEMENT Seqdesc_pdb (PDB-block)>

<!-- cofactor, etc associated but not bound -->
<!ELEMENT Seqdesc_het (Heterogen)>

<!-- source of materials, includes Org-ref -->
<!ELEMENT Seqdesc_source (BioSource)>

<!-- info on the molecule and techniques -->
<!ELEMENT Seqdesc_molinfo (MolInfo)>

<!-- model evidence for XM records -->
<!ELEMENT Seqdesc_modelev (ModelEvidenceSupport)>

<!--
******* NOTE:
*       mol-type, modif, method, and org are consolidated and expanded
*       in Org-ref, BioSource, and MolInfo in this specification. They
*       will be removed in later specifications. Do not use them in the
*       the future. Instead expect the new structures.
*
***************************
********************************************************************

 MolInfo gives information on the
 classification of the type and quality of the sequence

 WARNING: this will replace GIBB-mol, GIBB-mod, GIBB-method

********************************************************************
-->
<!ELEMENT MolInfo (
        MolInfo_biomol?, 
        MolInfo_tech?, 
        MolInfo_techexp?, 
        MolInfo_completeness?, 
        MolInfo_gbmoltype?)>

<!ELEMENT MolInfo_biomol (%INTEGER;)>

<!--
    pre-RNA	-  precursor RNA of any sort really
    other-genetic	-  other genetic material
    genomic-mRNA	-  reported a mix of genomic and cdna sequence
    cRNA	-  viral RNA genome copy intermediate
    snoRNA	-  small nucleolar RNA
    transcribed-RNA	-  transcribed RNA other than existing classes
-->
<!ATTLIST MolInfo_biomol value (
        unknown |
        genomic |
        pre-RNA |
        mRNA |
        rRNA |
        tRNA |
        snRNA |
        scRNA |
        peptide |
        other-genetic |
        genomic-mRNA |
        cRNA |
        snoRNA |
        transcribed-RNA |
        ncRNA |
        tmRNA |
        other
        ) #IMPLIED >


<!ELEMENT MolInfo_tech (%INTEGER;)>

<!--
    standard	-  standard sequencing
    est	-  Expressed Sequence Tag
    sts	-  Sequence Tagged Site
    survey	-  one-pass genomic sequence
    genemap	-  from genetic mapping techniques
    physmap	-  from physical mapping techniques
    derived	-  derived from other data, not a primary entity
    concept-trans	-  conceptual translation
    seq-pept	-  peptide was sequenced
    both	-  concept transl. w/ partial pept. seq.
    seq-pept-overlap	-  sequenced peptide, ordered by overlap
    seq-pept-homol	-  sequenced peptide, ordered by homology
    concept-trans-a	-  conceptual transl. supplied by author
    htgs-1	-  unordered High Throughput sequence contig
    htgs-2	-  ordered High Throughput sequence contig
    htgs-3	-  finished High Throughput sequence
    fli-cdna	-  full length insert cDNA
    htgs-0	-  single genomic reads for coordination
    htc	-  high throughput cDNA
    wgs	-  whole genome shotgun sequencing
    barcode	-  barcode of life project
    composite-wgs-htgs	-  composite of WGS and HTGS
    tsa	-  transcriptome shotgun assembly
    other	-  use Source.techexp
-->
<!ATTLIST MolInfo_tech value (
        unknown |
        standard |
        est |
        sts |
        survey |
        genemap |
        physmap |
        derived |
        concept-trans |
        seq-pept |
        both |
        seq-pept-overlap |
        seq-pept-homol |
        concept-trans-a |
        htgs-1 |
        htgs-2 |
        htgs-3 |
        fli-cdna |
        htgs-0 |
        htc |
        wgs |
        barcode |
        composite-wgs-htgs |
        tsa |
        other
        ) #IMPLIED >


<!--
 explanation if tech not enough

 Completeness is not indicated in most records.  For genomes, assume
 the sequences are incomplete unless specifically marked as complete.
 For mRNAs, assume the ends are not known exactly unless marked as
 having the left or right end.

-->
<!ELEMENT MolInfo_techexp (#PCDATA)>

<!ELEMENT MolInfo_completeness (%INTEGER;)>

<!--
    complete	-  complete biological entity
    partial	-  partial but no details given
    no-left	-  missing 5' or NH3 end
    no-right	-  missing 3' or COOH end
    no-ends	-  missing both ends
    has-left	-  5' or NH3 end present
    has-right	-  3' or COOH end present
-->
<!ATTLIST MolInfo_completeness value (
        unknown |
        complete |
        partial |
        no-left |
        no-right |
        no-ends |
        has-left |
        has-right |
        other
        ) #IMPLIED >


<!-- identifies particular ncRNA -->
<!ELEMENT MolInfo_gbmoltype (#PCDATA)>

<!-- type of molecule represented -->
<!ELEMENT GIBB-mol %ENUM;>

<!--
    pre-mRNA	-  precursor RNA of any sort really
    other-genetic	-  other genetic material
    genomic-mRNA	-  reported a mix of genomic and cdna sequence
-->
<!ATTLIST GIBB-mol value (
        unknown |
        genomic |
        pre-mRNA |
        mRNA |
        rRNA |
        tRNA |
        snRNA |
        scRNA |
        peptide |
        other-genetic |
        genomic-mRNA |
        other
        ) #REQUIRED >


<!-- GenInfo Backbone modifiers -->
<!ELEMENT GIBB-mod %ENUM;>

<!--
    mutagen	-  subject of mutagenesis ?
    natmut	-  natural mutant ?
    no-left	-  missing left end (5' for na, NH2 for aa)
    no-right	-  missing right end (3' or COOH)
    est	-  expressed sequence tag
    sts	-  sequence tagged site
    survey	-  one pass survey sequence
    genemap	-  is a genetic map
    restmap	-  is an ordered restriction map
    physmap	-  is a physical map (not ordered restriction map)
-->
<!ATTLIST GIBB-mod value (
        dna |
        rna |
        extrachrom |
        plasmid |
        mitochondrial |
        chloroplast |
        kinetoplast |
        cyanelle |
        synthetic |
        recombinant |
        partial |
        complete |
        mutagen |
        natmut |
        transposon |
        insertion-seq |
        no-left |
        no-right |
        macronuclear |
        proviral |
        est |
        sts |
        survey |
        chromoplast |
        genemap |
        restmap |
        physmap |
        other
        ) #REQUIRED >


<!-- sequencing methods -->
<!ELEMENT GIBB-method %ENUM;>

<!--
    concept-trans	-  conceptual translation
    seq-pept	-  peptide was sequenced
    both	-  concept transl. w/ partial pept. seq.
    seq-pept-overlap	-  sequenced peptide, ordered by overlap
    seq-pept-homol	-  sequenced peptide, ordered by homology
    concept-trans-a	-  conceptual transl. supplied by author
-->
<!ATTLIST GIBB-method value (
        concept-trans |
        seq-pept |
        both |
        seq-pept-overlap |
        seq-pept-homol |
        concept-trans-a |
        other
        ) #REQUIRED >


<!-- any display numbering system -->
<!ELEMENT Numbering (
        Numbering_cont | 
        Numbering_enum | 
        Numbering_ref | 
        Numbering_real)>

<!-- continuous numbering -->
<!ELEMENT Numbering_cont (Num-cont)>

<!-- enumerated names for residues -->
<!ELEMENT Numbering_enum (Num-enum)>

<!-- by reference to another sequence -->
<!ELEMENT Numbering_ref (Num-ref)>

<!-- supports mapping to a float system -->
<!ELEMENT Numbering_real (Num-real)>

<!-- continuous display numbering system -->
<!ELEMENT Num-cont (
        Num-cont_refnum?, 
        Num-cont_has-zero?, 
        Num-cont_ascending?)>

<!-- number assigned to first residue -->
<!ELEMENT Num-cont_refnum (%INTEGER;)>

<!-- 0 used? -->
<!ELEMENT Num-cont_has-zero EMPTY>
<!ATTLIST Num-cont_has-zero value ( true | false ) "false" >


<!-- ascending numbers? -->
<!ELEMENT Num-cont_ascending EMPTY>
<!ATTLIST Num-cont_ascending value ( true | false ) "true" >


<!-- any tags to residues -->
<!ELEMENT Num-enum (
        Num-enum_num, 
        Num-enum_names)>

<!-- number of tags to follow -->
<!ELEMENT Num-enum_num (%INTEGER;)>

<!-- the tags -->
<!ELEMENT Num-enum_names (Num-enum_names_E*)>


<!ELEMENT Num-enum_names_E (#PCDATA)>

<!-- by reference to other sequences -->
<!ELEMENT Num-ref (
        Num-ref_type, 
        Num-ref_aligns?)>
<!-- type of reference -->
<!ELEMENT Num-ref_type %ENUM;>

<!--
    sources	-  by segmented or const seq sources
    aligns	-  by alignments given below
-->
<!ATTLIST Num-ref_type value (
        not-set |
        sources |
        aligns
        ) #REQUIRED >


<!ELEMENT Num-ref_aligns (Seq-align)>

<!-- mapping to floating point system -->
<!ELEMENT Num-real (
        Num-real_a, 
        Num-real_b, 
        Num-real_units?)>

<!-- from an integer system used by Bioseq -->
<!ELEMENT Num-real_a (%REAL;)>

<!-- position = (a * int_position) + b -->
<!ELEMENT Num-real_b (%REAL;)>

<!ELEMENT Num-real_units (#PCDATA)>

<!-- how sequence presented in pub -->
<!ELEMENT Pubdesc (
        Pubdesc_pub, 
        Pubdesc_name?, 
        Pubdesc_fig?, 
        Pubdesc_num?, 
        Pubdesc_numexc?, 
        Pubdesc_poly-a?, 
        Pubdesc_maploc?, 
        Pubdesc_seq-raw?, 
        Pubdesc_align-group?, 
        Pubdesc_comment?, 
        Pubdesc_reftype?)>

<!-- the citation(s) -->
<!ELEMENT Pubdesc_pub (Pub-equiv)>

<!-- name used in paper -->
<!ELEMENT Pubdesc_name (#PCDATA)>

<!-- figure in paper -->
<!ELEMENT Pubdesc_fig (#PCDATA)>

<!-- numbering from paper -->
<!ELEMENT Pubdesc_num (Numbering)>

<!-- numbering problem with paper -->
<!ELEMENT Pubdesc_numexc EMPTY>
<!ATTLIST Pubdesc_numexc value ( true | false ) #REQUIRED >


<!-- poly A tail indicated in figure? -->
<!ELEMENT Pubdesc_poly-a EMPTY>
<!ATTLIST Pubdesc_poly-a value ( true | false ) #REQUIRED >


<!-- map location reported in paper -->
<!ELEMENT Pubdesc_maploc (#PCDATA)>

<!-- original sequence from paper -->
<!ELEMENT Pubdesc_seq-raw (#PCDATA)>

<!-- this seq aligned with others in paper -->
<!ELEMENT Pubdesc_align-group (%INTEGER;)>

<!-- any comment on this pub in context -->
<!ELEMENT Pubdesc_comment (#PCDATA)>
<!-- type of reference in a GenBank record -->
<!ELEMENT Pubdesc_reftype (%INTEGER;)>

<!--
    seq	-  refers to sequence
    sites	-  refers to unspecified features
    feats	-  refers to specified features
    no-target	-  nothing specified (EMBL)
-->
<!ATTLIST Pubdesc_reftype value (
        seq |
        sites |
        feats |
        no-target
        ) #IMPLIED >


<!-- cofactor, prosthetic group, inhibitor, etc -->
<!ELEMENT Heterogen (#PCDATA)>

<!--
*** Instances of sequences *******************************
*
 the sequence data itself
-->
<!ELEMENT Seq-inst (
        Seq-inst_repr, 
        Seq-inst_mol, 
        Seq-inst_length?, 
        Seq-inst_fuzz?, 
        Seq-inst_topology?, 
        Seq-inst_strand?, 
        Seq-inst_seq-data?, 
        Seq-inst_ext?, 
        Seq-inst_hist?)>
<!-- representation class -->
<!ELEMENT Seq-inst_repr %ENUM;>

<!--
    not-set	-  empty
    virtual	-  no seq data
    raw	-  continuous sequence
    seg	-  segmented sequence
    const	-  constructed sequence
    ref	-  reference to another sequence
    consen	-  consensus sequence or pattern
    map	-  ordered map of any kind
    delta	-  sequence made by changes (delta) to others
-->
<!ATTLIST Seq-inst_repr value (
        not-set |
        virtual |
        raw |
        seg |
        const |
        ref |
        consen |
        map |
        delta |
        other
        ) #REQUIRED >

<!-- molecule class in living organism -->
<!ELEMENT Seq-inst_mol %ENUM;>

<!--
    not-set	-    > cdna = rna
    na	-  just a nucleic acid
-->
<!ATTLIST Seq-inst_mol value (
        not-set |
        dna |
        rna |
        aa |
        na |
        other
        ) #REQUIRED >


<!-- length of sequence in residues -->
<!ELEMENT Seq-inst_length (%INTEGER;)>

<!-- length uncertainty -->
<!ELEMENT Seq-inst_fuzz (Int-fuzz)>
<!-- topology of molecule -->
<!ELEMENT Seq-inst_topology %ENUM;>

<!--
    tandem	-  some part of tandem repeat
-->
<!ATTLIST Seq-inst_topology value (
        not-set |
        linear |
        circular |
        tandem |
        other
        ) #REQUIRED >

<!-- strandedness in living organism -->
<!ELEMENT Seq-inst_strand %ENUM;>

<!--
    ss	-  single strand
    ds	-  double strand
    other	-  default ds for DNA, ss for RNA, pept
-->
<!ATTLIST Seq-inst_strand value (
        not-set |
        ss |
        ds |
        mixed |
        other
        ) #REQUIRED >


<!-- the sequence -->
<!ELEMENT Seq-inst_seq-data (Seq-data)>

<!-- extensions for special types -->
<!ELEMENT Seq-inst_ext (Seq-ext)>

<!-- sequence history -->
<!ELEMENT Seq-inst_hist (Seq-hist)>

<!--
*** Sequence Extensions **********************************
*  for representing more complex types
*  const type uses Seq-hist.assembly
-->
<!ELEMENT Seq-ext (
        Seq-ext_seg | 
        Seq-ext_ref | 
        Seq-ext_map | 
        Seq-ext_delta)>

<!-- segmented sequences -->
<!ELEMENT Seq-ext_seg (Seg-ext)>

<!-- hot link to another sequence (a view) -->
<!ELEMENT Seq-ext_ref (Ref-ext)>

<!-- ordered map of markers -->
<!ELEMENT Seq-ext_map (Map-ext)>

<!ELEMENT Seq-ext_delta (Delta-ext)>


<!ELEMENT Seg-ext (Seq-loc*)>


<!ELEMENT Ref-ext (Seq-loc)>


<!ELEMENT Map-ext (Seq-feat*)>


<!ELEMENT Delta-ext (Delta-seq*)>


<!ELEMENT Delta-seq (
        Delta-seq_loc | 
        Delta-seq_literal)>

<!-- point to a sequence -->
<!ELEMENT Delta-seq_loc (Seq-loc)>

<!-- a piece of sequence -->
<!ELEMENT Delta-seq_literal (Seq-literal)>


<!ELEMENT Seq-literal (
        Seq-literal_length, 
        Seq-literal_fuzz?, 
        Seq-literal_seq-data?)>

<!-- must give a length in residues -->
<!ELEMENT Seq-literal_length (%INTEGER;)>

<!-- could be unsure -->
<!ELEMENT Seq-literal_fuzz (Int-fuzz)>

<!-- may have the data -->
<!ELEMENT Seq-literal_seq-data (Seq-data)>

<!--
*** Sequence History Record ***********************************
** assembly = records how seq was assembled from others
** replaces = records sequences made obsolete by this one
** replaced-by = this seq is made obsolete by another(s)
-->
<!ELEMENT Seq-hist (
        Seq-hist_assembly?, 
        Seq-hist_replaces?, 
        Seq-hist_replaced-by?, 
        Seq-hist_deleted?)>

<!-- how was this assembled? -->
<!ELEMENT Seq-hist_assembly (Seq-align*)>

<!-- seq makes these seqs obsolete -->
<!ELEMENT Seq-hist_replaces (Seq-hist-rec)>

<!-- these seqs make this one obsolete -->
<!ELEMENT Seq-hist_replaced-by (Seq-hist-rec)>

<!ELEMENT Seq-hist_deleted (
        Seq-hist_deleted_bool | 
        Seq-hist_deleted_date)>

<!ELEMENT Seq-hist_deleted_bool EMPTY>
<!ATTLIST Seq-hist_deleted_bool value ( true | false ) #REQUIRED >


<!ELEMENT Seq-hist_deleted_date (Date)>


<!ELEMENT Seq-hist-rec (
        Seq-hist-rec_date?, 
        Seq-hist-rec_ids)>

<!ELEMENT Seq-hist-rec_date (Date)>

<!ELEMENT Seq-hist-rec_ids (Seq-id*)>

<!--
*** Various internal sequence representations ************
*      all are controlled, fixed length forms
 sequence representations
-->
<!ELEMENT Seq-data (
        Seq-data_iupacna | 
        Seq-data_iupacaa | 
        Seq-data_ncbi2na | 
        Seq-data_ncbi4na | 
        Seq-data_ncbi8na | 
        Seq-data_ncbipna | 
        Seq-data_ncbi8aa | 
        Seq-data_ncbieaa | 
        Seq-data_ncbipaa | 
        Seq-data_ncbistdaa | 
        Seq-data_gap)>

<!-- IUPAC 1 letter nuc acid code -->
<!ELEMENT Seq-data_iupacna (IUPACna)>

<!-- IUPAC 1 letter amino acid code -->
<!ELEMENT Seq-data_iupacaa (IUPACaa)>

<!-- 2 bit nucleic acid code -->
<!ELEMENT Seq-data_ncbi2na (NCBI2na)>

<!-- 4 bit nucleic acid code -->
<!ELEMENT Seq-data_ncbi4na (NCBI4na)>

<!-- 8 bit extended nucleic acid code -->
<!ELEMENT Seq-data_ncbi8na (NCBI8na)>

<!-- nucleic acid probabilities -->
<!ELEMENT Seq-data_ncbipna (NCBIpna)>

<!-- 8 bit extended amino acid codes -->
<!ELEMENT Seq-data_ncbi8aa (NCBI8aa)>

<!-- extended ASCII 1 letter aa codes -->
<!ELEMENT Seq-data_ncbieaa (NCBIeaa)>

<!-- amino acid probabilities -->
<!ELEMENT Seq-data_ncbipaa (NCBIpaa)>

<!-- consecutive codes for std aas -->
<!ELEMENT Seq-data_ncbistdaa (NCBIstdaa)>

<!-- gap types -->
<!ELEMENT Seq-data_gap (Seq-gap)>


<!ELEMENT Seq-gap (
        Seq-gap_type, 
        Seq-gap_linkage?, 
        Seq-gap_linkage-evidence?)>

<!ELEMENT Seq-gap_type (%INTEGER;)>

<!--
    fragment	-  Deprecated. Used only for AGP 1.1
    clone	-  Deprecated. Used only for AGP 1.1
-->
<!ATTLIST Seq-gap_type value (
        unknown |
        fragment |
        clone |
        short-arm |
        heterochromatin |
        centromere |
        telomere |
        repeat |
        contig |
        scaffold |
        other
        ) #IMPLIED >


<!ELEMENT Seq-gap_linkage (%INTEGER;)>
<!ATTLIST Seq-gap_linkage value (
        unlinked |
        linked |
        other
        ) #IMPLIED >


<!ELEMENT Seq-gap_linkage-evidence (Linkage-evidence*)>


<!ELEMENT Linkage-evidence (
        Linkage-evidence_type)>

<!ELEMENT Linkage-evidence_type (%INTEGER;)>
<!ATTLIST Linkage-evidence_type value (
        paired-ends |
        align-genus |
        align-xgenus |
        align-trnscpt |
        within-clone |
        clone-contig |
        map |
        strobe |
        unspecified |
        pcr |
        other
        ) #IMPLIED >


<!-- IUPAC 1 letter codes, no spaces -->
<!ELEMENT IUPACna (#PCDATA)>

<!-- IUPAC 1 letter codes, no spaces -->
<!ELEMENT IUPACaa (#PCDATA)>

<!-- 00=A, 01=C, 10=G, 11=T -->
<!ELEMENT NCBI2na (%OCTETS;)>

<!--
 1 bit each for agct
 0001=A, 0010=C, 0100=G, 1000=T/U
 0101=Purine, 1010=Pyrimidine, etc
-->
<!ELEMENT NCBI4na (%OCTETS;)>

<!-- for modified nucleic acids -->
<!ELEMENT NCBI8na (%OCTETS;)>

<!--
 5 octets/base, prob for a,c,g,t,n
 probabilities are coded 0-255 = 0.0-1.0
-->
<!ELEMENT NCBIpna (%OCTETS;)>

<!-- for modified amino acids -->
<!ELEMENT NCBI8aa (%OCTETS;)>

<!--
 ASCII extended 1 letter aa codes
 IUPAC codes + U=selenocysteine
-->
<!ELEMENT NCBIeaa (#PCDATA)>

<!--
 25 octets/aa, prob for IUPAC aas in order:
 A-Y,B,Z,X,(ter),anything
 probabilities are coded 0-255 = 0.0-1.0
-->
<!ELEMENT NCBIpaa (%OCTETS;)>

<!-- codes 0-25, 1 per byte -->
<!ELEMENT NCBIstdaa (%OCTETS;)>

<!--
*** Sequence Annotation *************************************
*
 This is a replica of Textseq-id
 This is specific for annotations, and exists to maintain a semantic
 difference between IDs assigned to annotations and IDs assigned to
 sequences
-->
<!ELEMENT Textannot-id (
        Textannot-id_name?, 
        Textannot-id_accession?, 
        Textannot-id_release?, 
        Textannot-id_version?)>

<!ELEMENT Textannot-id_name (#PCDATA)>

<!ELEMENT Textannot-id_accession (#PCDATA)>

<!ELEMENT Textannot-id_release (#PCDATA)>

<!ELEMENT Textannot-id_version (%INTEGER;)>


<!ELEMENT Annot-id (
        Annot-id_local | 
        Annot-id_ncbi | 
        Annot-id_general | 
        Annot-id_other)>

<!ELEMENT Annot-id_local (Object-id)>

<!ELEMENT Annot-id_ncbi (%INTEGER;)>

<!ELEMENT Annot-id_general (Dbtag)>
<!--
*** Sequence Annotation *************************************
*
 This is a replica of Textseq-id
 This is specific for annotations, and exists to maintain a semantic
 difference between IDs assigned to annotations and IDs assigned to
 sequences
-->
<!ELEMENT Annot-id_other (Textannot-id)>


<!ELEMENT Annot-descr (Annotdesc*)>


<!ELEMENT Annotdesc (
        Annotdesc_name | 
        Annotdesc_title | 
        Annotdesc_comment | 
        Annotdesc_pub | 
        Annotdesc_user | 
        Annotdesc_create-date | 
        Annotdesc_update-date | 
        Annotdesc_src | 
        Annotdesc_align | 
        Annotdesc_region)>

<!-- a short name for this collection -->
<!ELEMENT Annotdesc_name (#PCDATA)>

<!-- a title for this collection -->
<!ELEMENT Annotdesc_title (#PCDATA)>

<!-- a more extensive comment -->
<!ELEMENT Annotdesc_comment (#PCDATA)>

<!-- a reference to the publication -->
<!ELEMENT Annotdesc_pub (Pubdesc)>

<!-- user defined object -->
<!ELEMENT Annotdesc_user (User-object)>

<!-- date entry first created/released -->
<!ELEMENT Annotdesc_create-date (Date)>

<!-- date of last update -->
<!ELEMENT Annotdesc_update-date (Date)>

<!-- source sequence from which annot came -->
<!ELEMENT Annotdesc_src (Seq-id)>

<!-- definition of the SeqAligns -->
<!ELEMENT Annotdesc_align (Align-def)>

<!-- all contents cover this region -->
<!ELEMENT Annotdesc_region (Seq-loc)>


<!ELEMENT Align-def (
        Align-def_align-type, 
        Align-def_ids?)>
<!-- class of align Seq-annot -->
<!ELEMENT Align-def_align-type (%INTEGER;)>

<!--
    ref	-  set of alignments to the same sequence
    alt	-  set of alternate alignments of the same seqs
    blocks	-  set of aligned blocks in the same seqs
-->
<!ATTLIST Align-def_align-type value (
        ref |
        alt |
        blocks |
        other
        ) #IMPLIED >


<!-- used for the one ref seqid for now -->
<!ELEMENT Align-def_ids (Seq-id*)>

<!-- features in table form -->
<!ELEMENT Seq-annot (
        Seq-annot_id?, 
        Seq-annot_db?, 
        Seq-annot_name?, 
        Seq-annot_desc?, 
        Seq-annot_data)>

<!ELEMENT Seq-annot_id (Annot-id*)>
<!-- source of annotation -->
<!ELEMENT Seq-annot_db (%INTEGER;)>
<!ATTLIST Seq-annot_db value (
        genbank |
        embl |
        ddbj |
        pir |
        sp |
        bbone |
        pdb |
        other
        ) #IMPLIED >


<!-- source if "other" above -->
<!ELEMENT Seq-annot_name (#PCDATA)>

<!-- used only for stand alone Seq-annots -->
<!ELEMENT Seq-annot_desc (Annot-descr)>

<!ELEMENT Seq-annot_data (
        Seq-annot_data_ftable | 
        Seq-annot_data_align | 
        Seq-annot_data_graph | 
        Seq-annot_data_ids | 
        Seq-annot_data_locs | 
        Seq-annot_data_seq-table)>

<!ELEMENT Seq-annot_data_ftable (Seq-feat*)>

<!ELEMENT Seq-annot_data_align (Seq-align*)>

<!ELEMENT Seq-annot_data_graph (Seq-graph*)>

<!-- used for communication between tools -->
<!ELEMENT Seq-annot_data_ids (Seq-id*)>

<!-- used for communication between tools -->
<!ELEMENT Seq-annot_data_locs (Seq-loc*)>

<!ELEMENT Seq-annot_data_seq-table (Seq-table)>

