1NCBI-BlastOutput2 DEFINITIONS ::= 2BEGIN 3 4BlastOutput2 ::= SEQUENCE { 5 report Report OPTIONAL, 6 error Err OPTIONAL 7} 8 9BlastXML2 ::= SET OF BlastOutput2 10 11Report ::= SEQUENCE { 12 program VisibleString , -- BLAST program: blastp, tblastx etc. 13 version VisibleString , -- Program version 14 reference VisibleString , -- Steven, David, Tom and others 15 search-target Target, 16 params Parameters, -- search parameters 17 results Results 18} 19 20Err ::= SEQUENCE { 21 code INTEGER, 22 message VisibleString OPTIONAL 23} 24 25Target ::= CHOICE { 26 db VisibleString , -- BLAST Database name 27 subjects SEQUENCE OF VisibleString -- Subject IDs 28} 29 30Results ::=CHOICE { 31 iterations SEQUENCE OF Iteration , 32 -- iterative search (psi and delta blast) 33 search Search, -- db search 34 bl2seq SEQUENCE OF Search -- bl2seq 35} 36 37Iteration ::= SEQUENCE { 38 iter-num INTEGER, -- iteration number (use with psiblast) 39 search Search 40} 41 42Search ::= SEQUENCE { 43 query-id VisibleString OPTIONAL, -- SeqId of query 44 query-title VisibleString OPTIONAL, -- Definition line of query 45 query-len INTEGER OPTIONAL , -- length of query sequence 46 query-masking SEQUENCE OF Range OPTIONAL, -- Masked offsets. 47 hits SEQUENCE OF Hit OPTIONAL, -- Hits one for every db sequence 48 stat Statistics OPTIONAL, -- search statistics 49 message VisibleString OPTIONAL -- Some (error?) information 50} 51 52Parameters ::= SEQUENCE { 53 matrix VisibleString OPTIONAL , -- Matrix used (-M) 54 expect REAL , -- Expectation threshold (-e) 55 include REAL OPTIONAL , -- Inclusion threshold (-h) 56 sc-match INTEGER OPTIONAL , -- match score for NT (-r) 57 sc-mismatch INTEGER OPTIONAL , -- mismatch score for NT (-q) 58 gap-open INTEGER OPTIONAL, -- Gap opening cost (-G) 59 gap-extend INTEGER OPTIONAL, -- Gap extension cost (-E) 60 filter VisibleString OPTIONAL, -- Filtering options (-F) 61 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern 62 entrez-query VisibleString OPTIONAL, -- Limit of request to Entrez query 63 cbs INTEGER OPTIONAL, -- composition-based stats (numbers correspond to 64 -- numbering in stand-alone application parameter -comp_based_stats). 65 query-gencode INTEGER OPTIONAL, -- genetic code for query (blastx or tblastx) 66 db-gencode INTEGER OPTIONAL, -- genetic code for db or subjects (tblastn or tblastx) 67 bl2seq-mode VisibleString OPTIONAL -- bl2seq mode 68} 69 70-- Used to specify start/stop of masking on query. 71Range ::= SEQUENCE { 72 from INTEGER, -- Beginning of masked range (one-offset) 73 to INTEGER -- End of masked range (one-offset) 74} 75 76Statistics ::= SEQUENCE { 77 db-num BigInt OPTIONAL, -- Number of sequences in BLAST db 78 db-len BigInt OPTIONAL, -- Length of BLAST db 79 hsp-len INTEGER , -- Effective HSP length 80 eff-space BigInt, -- Effective search space 81 kappa REAL, -- Karlin-Altschul parameter K 82 lambda REAL, -- Karlin-Altschul parameter Lambda 83 entropy REAL -- Karlin-Altschul parameter H 84} 85 86-- Description of entries for this (possibly non-redundant) sequence. 87HitDescr ::= SEQUENCE { 88 id VisibleString , -- SeqId of subject 89 accession VisibleString OPTIONAL, -- accession 90 title VisibleString OPTIONAL, -- title (definition line) of subject 91 taxid INTEGER OPTIONAL, -- NCBI taxid (9606 for human) 92 sciname VisibleString OPTIONAL -- binomial scientific name ("Homo sapiens" for human). 93} 94 95Hit ::= SEQUENCE { 96 num INTEGER , -- hit number 97 description SEQUENCE OF HitDescr, -- ID, title, and taxonomy for each entry in the PIG 98 len INTEGER , -- length of subject 99 hsps SEQUENCE OF Hsp OPTIONAL -- all HSP regions for the given subject 100} 101 102Hsp ::= SEQUENCE { 103 num INTEGER , -- HSP number 104 bit-score REAL , -- score (in bits) of HSP 105 score REAL , -- score of HSP 106 evalue REAL , -- e-value of HSP 107 identity INTEGER OPTIONAL , -- number of identities in HSP 108 positive INTEGER OPTIONAL , -- number of positives in HSP 109 density INTEGER OPTIONAL , -- score density 110 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern 111 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern 112 query-from INTEGER , -- start of HSP in query 113 query-to INTEGER , -- end of HSP 114 query-strand VisibleString OPTIONAL, -- Strand of query (blastn) 115 query-frame INTEGER OPTIONAL , -- translation frame of query (blastx, tblastx) 116 hit-from INTEGER, -- start of HSP in subject 117 hit-to INTEGER , -- end of HSP in subject 118 hit-strand VisibleString OPTIONAL, -- Strand of subject (blastn) 119 hit-frame INTEGER OPTIONAL , -- translation frame of subject (tblastn, tblastx) 120 align-len INTEGER OPTIONAL , -- length of the alignment used 121 gaps INTEGER OPTIONAL , -- number of gaps in HSP 122 qseq VisibleString , -- alignment string for the query (with gaps) 123 hseq VisibleString, -- alignment string for subject (with gaps) 124 midline VisibleString OPTIONAL -- formating middle line 125} 126 127END 128