src/objects/blastxml2/blastxml2.asn

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NCBI-BlastOutput2 DEFINITIONS ::=
BEGIN

BlastOutput2 ::= SEQUENCE {
	report Report OPTIONAL,
	error  Err OPTIONAL
}

BlastXML2 ::= SET OF BlastOutput2

Report ::= SEQUENCE {
	program VisibleString ,		-- BLAST program: blastp, tblastx etc.
	version VisibleString ,		-- Program version 
	reference VisibleString ,	-- Steven, David, Tom and others
	search-target Target,
	params Parameters,		-- search parameters
	results Results
}

Err ::= SEQUENCE {
	code                    INTEGER,
	message                 VisibleString OPTIONAL
}

Target ::= CHOICE {
	db VisibleString ,			-- BLAST Database name
	subjects SEQUENCE OF VisibleString 	-- Subject IDs
}

Results ::=CHOICE {
    iterations SEQUENCE OF Iteration , 
                                --  iterative search (psi and delta blast)
    search Search, 	        --  db search   
    bl2seq SEQUENCE OF Search   --  bl2seq
}

Iteration ::= SEQUENCE {
	iter-num INTEGER,	 -- iteration number (use with psiblast)
	search Search
}

Search ::= SEQUENCE {
	query-id VisibleString OPTIONAL,           -- SeqId of query
	query-title VisibleString OPTIONAL,        -- Definition line of query
	query-len INTEGER OPTIONAL ,	           -- length of query sequence
	query-masking SEQUENCE OF Range OPTIONAL,  -- Masked offsets.
	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 OPTIONAL,          -- Gap opening cost (-G)
	gap-extend INTEGER OPTIONAL,	    -- 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
	cbs INTEGER OPTIONAL,	 	    -- composition-based stats (numbers correspond to
					    -- numbering in stand-alone application parameter -comp_based_stats).
	query-gencode INTEGER OPTIONAL,     -- genetic code for query (blastx or tblastx)
	db-gencode INTEGER OPTIONAL,	    -- genetic code for db or subjects (tblastn or tblastx)
	bl2seq-mode VisibleString OPTIONAL  -- bl2seq mode 
}

-- Used to specify start/stop of masking on query.
Range ::= SEQUENCE {
	from INTEGER,			-- Beginning of masked range (one-offset)
	to INTEGER			-- End of masked range (one-offset)
}

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

-- Description of entries for this (possibly non-redundant) sequence.
HitDescr ::= SEQUENCE {
	id VisibleString ,	        -- SeqId of subject
	accession VisibleString OPTIONAL,     -- accession
	title VisibleString OPTIONAL,   -- title (definition line) of subject
	taxid INTEGER OPTIONAL,		-- NCBI taxid (9606 for human)
	sciname VisibleString OPTIONAL	-- binomial scientific name ("Homo sapiens" for human).  
}

Hit ::= SEQUENCE {
	num INTEGER , 			    -- hit number
	description SEQUENCE OF HitDescr,   -- ID, title, and taxonomy for each entry in the PIG
	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
	identity INTEGER OPTIONAL ,	-- number of identities in HSP
	positive INTEGER OPTIONAL ,	-- number of positives in HSP
	density INTEGER OPTIONAL ,	-- score density
	pattern-from INTEGER OPTIONAL ,	-- start of PHI-BLAST pattern
	pattern-to INTEGER OPTIONAL ,	-- end of PHI-BLAST pattern
	query-from INTEGER ,	        -- start of HSP in query
	query-to INTEGER ,		-- end of HSP
	query-strand VisibleString OPTIONAL, -- Strand of query (blastn)
	query-frame INTEGER OPTIONAL ,	-- translation frame of query (blastx, tblastx)
	hit-from INTEGER,		-- start of HSP in subject
	hit-to INTEGER ,		-- end of HSP in subject
	hit-strand VisibleString OPTIONAL, -- Strand of subject (blastn)
	hit-frame INTEGER OPTIONAL ,	-- translation frame of subject (tblastn, tblastx)
	align-len INTEGER OPTIONAL ,	-- length of the alignment used
	gaps INTEGER OPTIONAL ,		-- number of gaps in HSP
	qseq VisibleString ,		-- alignment string for the query (with gaps)
	hseq VisibleString,		-- alignment string for subject (with gaps)
	midline VisibleString OPTIONAL	-- formating middle line
}

END