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<!-- ============================================
::DATATOOL:: Generated from "blastdb.asn"
::DATATOOL:: by application DATATOOL version 2.3.1
::DATATOOL:: on 07/15/2011 23:04:47
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-BlastDL"
================================================= -->
<!--
$Id: blastdb.asn 311249 2011-07-11 14:12:16Z camacho $
Notes:
taxonomy: an integer is proposed, which would require some sort of
table (or network connection) to do the conversions from integer
to various names. This could save quite a bit of space for databases
that are predominantly of one organism (e.g., human in htgs).
I've proposed here that table contain scientific-, common-, and
blast-names at the advice of Scott Federhen. Scott also was in
favor of having the complete lineage in the file, but it seems like
this would be seldom used and we could have a view with a link back
to the taxonomy page for anyone needing it. Since one file would
suffice for all blast databases, it seems like this should be a new file.
memberships: a sequence of integers is proposed. Each bit of an integer
would indicate membership in some (virtual) blast database (e.g., pdb,
swissprot) or some classification (e.g., mRNA, genomic).
links: a sequence of integers is proposed. Each bit of an integer would
indicate a link that could be established based upon the gi of the
database sequence.
-->
<!-- Elements used by other modules:
Blast-def-line-set,
Blast-def-line -->
<!-- Elements referenced from other modules:
Seq-id,
Seq-loc FROM NCBI-Seqloc -->
<!-- ============================================ -->
<!-- all deflines for an entry -->
<!ELEMENT Blast-def-line-set (Blast-def-line*)>
<!ELEMENT Blast-def-line (
Blast-def-line_title?,
Blast-def-line_seqid,
Blast-def-line_taxid?,
Blast-def-line_memberships?,
Blast-def-line_links?,
Blast-def-line_other-info?)>
<!-- simple title -->
<!ELEMENT Blast-def-line_title (#PCDATA)>
<!-- Regular NCBI Seq-Id -->
<!ELEMENT Blast-def-line_seqid (Seq-id*)>
<!-- taxonomy id -->
<!ELEMENT Blast-def-line_taxid (%INTEGER;)>
<!-- bit arrays -->
<!ELEMENT Blast-def-line_memberships (Blast-def-line_memberships_E*)>
<!ELEMENT Blast-def-line_memberships_E (%INTEGER;)>
<!-- DEPRECATED, replaced by LinkoutDB -->
<!ELEMENT Blast-def-line_links (Blast-def-line_links_E*)>
<!ELEMENT Blast-def-line_links_E (%INTEGER;)>
<!-- for future use (probably genomic sequences) -->
<!ELEMENT Blast-def-line_other-info (Blast-def-line_other-info_E*)>
<!ELEMENT Blast-def-line_other-info_E (%INTEGER;)>
<!--
This defines the possible sequence filtering algorithms to be used in a
BLAST database
-->
<!ELEMENT Blast-filter-program (%INTEGER;)>
<!ATTLIST Blast-filter-program value (
not-set |
dust |
seg |
windowmasker |
repeat |
other |
max
) #IMPLIED >
<!ELEMENT Blast-mask-list (
Blast-mask-list_masks,
Blast-mask-list_more)>
<!-- masks for a single sequence should be grouped in a Packed-seqint -->
<!ELEMENT Blast-mask-list_masks (Seq-loc*)>
<!--
as of 01/21/2010, this field is set to false always, indicating that the
entire object (set of Seq-loc) is contained in this object
-->
<!ELEMENT Blast-mask-list_more EMPTY>
<!ATTLIST Blast-mask-list_more value ( true | false ) #REQUIRED >
<!-- Defines the masking information for a set of sequences -->
<!ELEMENT Blast-db-mask-info (
Blast-db-mask-info_algo-id,
Blast-db-mask-info_algo-program,
Blast-db-mask-info_algo-options,
Blast-db-mask-info_masks)>
<!ELEMENT Blast-db-mask-info_algo-id (%INTEGER;)>
<!--
This defines the possible sequence filtering algorithms to be used in a
BLAST database
-->
<!ELEMENT Blast-db-mask-info_algo-program (Blast-filter-program)>
<!ELEMENT Blast-db-mask-info_algo-options (#PCDATA)>
<!--
This object was originally created to allow pagination of the sequence
masks, but this feature was discontinued in 01/21/2010
-->
<!ELEMENT Blast-db-mask-info_masks (Blast-mask-list)>
|
