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