1--$Id: blstxml.asn,v 1.1 2002/12/02 19:43:46 dondosha Exp $ 2-- 3--$Revision: 1.1 $ 4--********************************************************************** 5-- 6-- ASN.1 for simplified BLAST output in XML 7-- by James Ostell, Yuri Wolf and Sergey Shavirin, 2000 8-- 9-- 10-- $Log: blstxml.asn,v $ 11-- Revision 1.1 2002/12/02 19:43:46 dondosha 12-- Copy of the namesake file in distrib/tools CVS directory 13-- 14-- Revision 1.1 2002/12/02 19:42:22 dondosha 15-- Copy of the namesake file in distrib/tools CVS directory 16-- 17-- Revision 6.7 2002/07/17 22:28:13 dondosha 18-- Added support for megablast XML output 19-- 20-- Revision 6.6 2001/05/03 17:52:16 shavirin 21-- Adopted for usage with mani-iterational XML definition. 22-- 23-- Revision 6.4 2000/11/08 20:07:20 shavirin 24-- Added new parameter align_len analogos to the number reported in 25-- the Traditional Blast Output. 26-- 27-- Revision 6.3 2000/10/23 20:24:03 shavirin 28-- Few parameters were changed to OPTIONAL to allow XML without results: 29-- failure or no hits found condition. 30-- 31-- Revision 6.2 2000/08/11 17:48:35 shavirin 32-- Small fix. 33-- 34-- Revision 6.1 2000/08/09 20:43:12 shavirin 35-- Initial revision. 36-- 37-- 38--********************************************************************** 39 40NCBI-BlastOutput DEFINITIONS ::= 41BEGIN 42 43BlastOutput ::= SEQUENCE { 44 program VisibleString , -- BLAST program: blastp, tblastx etc. 45 version VisibleString , -- Program version 46 reference VisibleString , -- Steven, David, Tom and others 47 db VisibleString , -- BLAST Database name 48 query-ID VisibleString , -- SeqId of query 49 query-def VisibleString , -- Definition line of query 50 query-len INTEGER , -- length of query sequence 51 query-seq VisibleString OPTIONAL , -- query sequence itself 52 param Parameters, -- search parameters 53 iterations SEQUENCE OF Iteration, 54 mbstat Statistics OPTIONAL -- Mega BLAST search statistics 55} 56Iteration ::= SEQUENCE { 57 iter-num INTEGER , -- iteration number 58 query-ID VisibleString OPTIONAL, -- SeqId of query 59 query-def VisibleString OPTIONAL,-- Definition line of query 60 query-len INTEGER OPTIONAL , -- length of query sequence 61 hits SEQUENCE OF Hit OPTIONAL, -- Hits one for every db sequence 62 stat Statistics OPTIONAL, -- search statistics 63 message VisibleString OPTIONAL -- Some (error?) information 64} 65Parameters ::= SEQUENCE { 66 matrix VisibleString OPTIONAL , -- Matrix used (-M) 67 expect REAL , -- Expectation threshold (-e) 68 include REAL OPTIONAL , -- Inclusion threshold (-h) 69 sc-match INTEGER OPTIONAL , -- match score for NT (-r) 70 sc-mismatch INTEGER OPTIONAL , -- mismatch score for NT (-q) 71 gap-open INTEGER , -- Gap opening cost (-G) 72 gap-extend INTEGER , -- Gap extension cost (-E) 73 filter VisibleString OPTIONAL, -- Filtering options (-F) 74 pattern VisibleString OPTIONAL, -- PHI-BLAST pattern 75 entrez-query VisibleString OPTIONAL -- Limit of request to Entrez query 76} 77 78Statistics ::= SEQUENCE { 79 db-num INTEGER , -- Number of sequences in BLAST db 80 db-len INTEGER , -- Length of BLAST db 81 hsp-len INTEGER , -- Effective HSP length 82 eff-space REAL, -- Effective search space 83 kappa REAL, -- Karlin-Altschul parameter K 84 lambda REAL, -- Karlin-Altschul parameter Lambda 85 entropy REAL -- Karlin-Altschul parameter H 86} 87 88Hit ::= SEQUENCE { 89 num INTEGER , -- hit number 90 id VisibleString , -- SeqId of subject 91 def VisibleString , -- definition line of subject 92 accession VisibleString , -- accession 93 len INTEGER , -- length of subject 94 hsps SEQUENCE OF Hsp OPTIONAL -- all HSP regions for the given subject 95} 96 97Hsp ::= SEQUENCE { 98 num INTEGER , -- HSP number 99 bit-score REAL , -- score (in bits) of HSP 100 score REAL , -- score of HSP 101 evalue REAL , -- e-value of HSP 102 query-from INTEGER , -- start of HSP in query 103 query-to INTEGER , -- end of HSP 104 hit-from INTEGER, -- start of HSP in subject 105 hit-to INTEGER , -- end of HSP in subject 106 pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern 107 pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern 108 query-frame INTEGER OPTIONAL , -- translation frame of query 109 hit-frame INTEGER OPTIONAL , -- translation frame of subject 110 identity INTEGER OPTIONAL , -- number of identities in HSP 111 positive INTEGER OPTIONAL , -- number of positives in HSP 112 gaps INTEGER OPTIONAL , -- number of gaps in HSP 113 align-len INTEGER OPTIONAL , -- length of the alignment used 114 density INTEGER OPTIONAL , -- score density 115 qseq VisibleString , -- alignment string for the query (with gaps) 116 hseq VisibleString, -- alignment string for subject (with gaps) 117 midline VisibleString OPTIONAL -- formating middle line 118} 119 120END 121