1--$Id: blastxml.asn 120927 2008-02-28 18:57:30Z ucko $
2
3NCBI-BlastOutput DEFINITIONS ::=
4BEGIN
5
6BlastOutput ::= SEQUENCE {
7	program VisibleString ,		-- BLAST program: blastp, tblastx etc.
8	version VisibleString ,		-- Program version
9	reference VisibleString ,	-- Steven, David, Tom and others
10	db VisibleString ,		-- BLAST Database name
11	query-ID VisibleString ,	-- SeqId of query
12	query-def VisibleString ,	-- Definition line of query
13	query-len INTEGER ,		-- length of query sequence
14	query-seq VisibleString OPTIONAL ,	-- query sequence itself
15	param Parameters,		-- search parameters
16        iterations SEQUENCE OF Iteration,
17        mbstat Statistics OPTIONAL        -- Mega BLAST search statistics
18}
19Iteration ::= SEQUENCE {
20	iter-num INTEGER ,	         -- iteration number
21	query-ID VisibleString OPTIONAL, -- SeqId of query
22	query-def VisibleString OPTIONAL,-- Definition line of query
23	query-len INTEGER OPTIONAL ,	 -- length of query sequence
24	hits SEQUENCE OF Hit OPTIONAL,	 -- Hits one for every db sequence
25	stat Statistics OPTIONAL,	 -- search statistics
26        message VisibleString OPTIONAL   -- Some (error?) information
27}
28Parameters ::= SEQUENCE {
29	matrix VisibleString OPTIONAL ,	-- Matrix used (-M)
30	expect REAL ,			-- Expectation threshold (-e)
31	include REAL OPTIONAL ,		-- Inclusion threshold (-h)
32	sc-match INTEGER OPTIONAL ,	-- match score for NT (-r)
33	sc-mismatch INTEGER OPTIONAL ,	-- mismatch score for NT (-q)
34	gap-open INTEGER ,		-- Gap opening cost (-G)
35	gap-extend INTEGER ,		-- Gap extension cost (-E)
36	filter VisibleString OPTIONAL,  -- Filtering options (-F)
37	pattern VisibleString OPTIONAL,	-- PHI-BLAST pattern
38        entrez-query VisibleString OPTIONAL -- Limit of request to Entrez query
39}
40
41Statistics ::= SEQUENCE {
42	db-num INTEGER ,		-- Number of sequences in BLAST db
43	db-len BigInt ,	                -- Length of BLAST db
44	hsp-len INTEGER ,		-- Effective HSP length
45	eff-space REAL,			-- Effective search space
46        kappa REAL,                     -- Karlin-Altschul parameter K
47        lambda REAL,                    -- Karlin-Altschul parameter Lambda
48        entropy REAL                    -- Karlin-Altschul parameter H
49}
50
51Hit ::= SEQUENCE {
52	num INTEGER ,			-- hit number
53	id VisibleString ,		-- SeqId of subject
54	def VisibleString ,		-- definition line of subject
55	accession VisibleString ,       -- accession
56	len INTEGER ,			-- length of subject
57	hsps SEQUENCE OF Hsp OPTIONAL	-- all HSP regions for the given subject
58}
59
60Hsp ::= SEQUENCE {
61	num INTEGER ,			-- HSP number
62	bit-score REAL ,		-- score (in bits) of HSP
63	score REAL ,			-- score of HSP
64	evalue REAL ,			-- e-value of HSP
65	query-from INTEGER ,		-- start of HSP in query
66	query-to INTEGER ,		-- end of HSP
67	hit-from INTEGER,		-- start of HSP in subject
68	hit-to INTEGER ,		-- end of HSP in subject
69	pattern-from INTEGER OPTIONAL ,	-- start of PHI-BLAST pattern
70	pattern-to INTEGER OPTIONAL ,	-- end of PHI-BLAST pattern
71	query-frame INTEGER OPTIONAL ,	-- translation frame of query
72	hit-frame INTEGER OPTIONAL ,	-- translation frame of subject
73	identity INTEGER OPTIONAL ,	-- number of identities in HSP
74	positive INTEGER OPTIONAL ,	-- number of positives in HSP
75	gaps INTEGER OPTIONAL ,		-- number of gaps in HSP
76	align-len INTEGER OPTIONAL ,	-- length of the alignment used
77	density INTEGER OPTIONAL ,	-- score density
78	qseq VisibleString ,		-- alignment string for the query (with gaps)
79	hseq VisibleString,		-- alignment string for subject (with gaps)
80	midline VisibleString OPTIONAL	-- formating middle line
81}
82
83END
84