--$Id: blastxml.asn 120927 2008-02-28 18:57:30Z ucko $

NCBI-BlastOutput DEFINITIONS ::=
BEGIN

BlastOutput ::= SEQUENCE {
	program VisibleString ,		-- BLAST program: blastp, tblastx etc.
	version VisibleString ,		-- Program version 
	reference VisibleString ,	-- Steven, David, Tom and others
	db VisibleString ,		-- BLAST Database name
	query-ID VisibleString ,	-- SeqId of query
	query-def VisibleString ,	-- Definition line of query
	query-len INTEGER ,		-- length of query sequence
	query-seq VisibleString OPTIONAL ,	-- query sequence itself
	param Parameters,		-- search parameters
        iterations SEQUENCE OF Iteration,
        mbstat Statistics OPTIONAL        -- Mega BLAST search statistics
}
Iteration ::= SEQUENCE {
	iter-num INTEGER ,	         -- iteration number
	query-ID VisibleString OPTIONAL, -- SeqId of query
	query-def VisibleString OPTIONAL,-- Definition line of query
	query-len INTEGER OPTIONAL ,	 -- length of query sequence
	hits SEQUENCE OF Hit OPTIONAL,	 -- Hits one for every db sequence
	stat Statistics OPTIONAL,	 -- search statistics            
        message VisibleString OPTIONAL   -- Some (error?) information
}
Parameters ::= SEQUENCE {
	matrix VisibleString OPTIONAL ,	-- Matrix used (-M)
	expect REAL ,			-- Expectation threshold (-e)
	include REAL OPTIONAL ,		-- Inclusion threshold (-h)
	sc-match INTEGER OPTIONAL ,	-- match score for NT (-r)
	sc-mismatch INTEGER OPTIONAL ,	-- mismatch score for NT (-q)
	gap-open INTEGER ,		-- Gap opening cost (-G)
	gap-extend INTEGER ,		-- Gap extension cost (-E)
	filter VisibleString OPTIONAL,  -- Filtering options (-F)
	pattern VisibleString OPTIONAL,	-- PHI-BLAST pattern
        entrez-query VisibleString OPTIONAL -- Limit of request to Entrez query
}

Statistics ::= SEQUENCE {
	db-num INTEGER ,		-- Number of sequences in BLAST db
	db-len BigInt ,	                -- Length of BLAST db
	hsp-len INTEGER ,		-- Effective HSP length
	eff-space REAL,			-- Effective search space
        kappa REAL,                     -- Karlin-Altschul parameter K
        lambda REAL,                    -- Karlin-Altschul parameter Lambda
        entropy REAL                    -- Karlin-Altschul parameter H
}       

Hit ::= SEQUENCE {
	num INTEGER ,			-- hit number
	id VisibleString ,		-- SeqId of subject
	def VisibleString ,		-- definition line of subject
	accession VisibleString ,       -- accession
	len INTEGER ,			-- length of subject
	hsps SEQUENCE OF Hsp OPTIONAL	-- all HSP regions for the given subject
}

Hsp ::= SEQUENCE {
	num INTEGER ,			-- HSP number
	bit-score REAL ,		-- score (in bits) of HSP
	score REAL ,			-- score of HSP
	evalue REAL ,			-- e-value of HSP
	query-from INTEGER ,		-- start of HSP in query
	query-to INTEGER ,		-- end of HSP
	hit-from INTEGER,		-- start of HSP in subject
	hit-to INTEGER ,		-- end of HSP in subject
	pattern-from INTEGER OPTIONAL ,	-- start of PHI-BLAST pattern
	pattern-to INTEGER OPTIONAL ,	-- end of PHI-BLAST pattern
	query-frame INTEGER OPTIONAL ,	-- translation frame of query
	hit-frame INTEGER OPTIONAL ,	-- translation frame of subject
	identity INTEGER OPTIONAL ,	-- number of identities in HSP
	positive INTEGER OPTIONAL ,	-- number of positives in HSP
	gaps INTEGER OPTIONAL ,		-- number of gaps in HSP
	align-len INTEGER OPTIONAL ,	-- length of the alignment used
	density INTEGER OPTIONAL ,	-- score density
	qseq VisibleString ,		-- alignment string for the query (with gaps)
	hseq VisibleString,		-- alignment string for subject (with gaps)
	midline VisibleString OPTIONAL	-- formating middle line
}

END