NCBI C Toolkit Cross Reference

C/tools/blstxml.asn

  1 --$Id: blstxml.asn,v 6.9 2008/08/26 22:25:36 kazimird Exp $
  2 
  3 NCBI-BlastOutput DEFINITIONS ::=
  4 BEGIN
  5 
  6 BlastOutput ::= 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 }
 19 Iteration ::= 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 }
 28 Parameters ::= 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 
 41 Statistics ::= 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 
 51 Hit ::= 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 
 60 Hsp ::= 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 
 83 END
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