87 lines
3.6 KiB
Groff
87 lines
3.6 KiB
Groff
--$Id: blastxml.asn 100080 2007-03-12 16:05:35Z kazimird $
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NCBI-BlastOutput DEFINITIONS ::=
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BEGIN
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-- pycrate patch, taken from general.asn
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BigInt ::= [APPLICATION 2] IMPLICIT INTEGER
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BlastOutput ::= SEQUENCE {
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program VisibleString , -- BLAST program: blastp, tblastx etc.
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version VisibleString , -- Program version
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reference VisibleString , -- Steven, David, Tom and others
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db VisibleString , -- BLAST Database name
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query-ID VisibleString , -- SeqId of query
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query-def VisibleString , -- Definition line of query
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query-len INTEGER , -- length of query sequence
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query-seq VisibleString OPTIONAL , -- query sequence itself
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param Parameters, -- search parameters
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iterations SEQUENCE OF Iteration,
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mbstat Statistics OPTIONAL -- Mega BLAST search statistics
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}
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Iteration ::= SEQUENCE {
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iter-num INTEGER , -- iteration number
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query-ID VisibleString OPTIONAL, -- SeqId of query
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query-def VisibleString OPTIONAL,-- Definition line of query
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query-len INTEGER OPTIONAL , -- length of query sequence
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hits SEQUENCE OF Hit OPTIONAL, -- Hits one for every db sequence
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stat Statistics OPTIONAL, -- search statistics
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message VisibleString OPTIONAL -- Some (error?) information
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}
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Parameters ::= SEQUENCE {
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matrix VisibleString OPTIONAL , -- Matrix used (-M)
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expect REAL , -- Expectation threshold (-e)
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include REAL OPTIONAL , -- Inclusion threshold (-h)
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sc-match INTEGER OPTIONAL , -- match score for NT (-r)
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sc-mismatch INTEGER OPTIONAL , -- mismatch score for NT (-q)
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gap-open INTEGER , -- Gap opening cost (-G)
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gap-extend INTEGER , -- Gap extension cost (-E)
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filter VisibleString OPTIONAL, -- Filtering options (-F)
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pattern VisibleString OPTIONAL, -- PHI-BLAST pattern
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entrez-query VisibleString OPTIONAL -- Limit of request to Entrez query
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}
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Statistics ::= SEQUENCE {
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db-num INTEGER , -- Number of sequences in BLAST db
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db-len BigInt , -- Length of BLAST db
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hsp-len INTEGER , -- Effective HSP length
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eff-space REAL, -- Effective search space
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kappa REAL, -- Karlin-Altschul parameter K
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lambda REAL, -- Karlin-Altschul parameter Lambda
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entropy REAL -- Karlin-Altschul parameter H
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}
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Hit ::= SEQUENCE {
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num INTEGER , -- hit number
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id VisibleString , -- SeqId of subject
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def VisibleString , -- definition line of subject
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accession VisibleString , -- accession
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len INTEGER , -- length of subject
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hsps SEQUENCE OF Hsp OPTIONAL -- all HSP regions for the given subject
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}
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Hsp ::= SEQUENCE {
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num INTEGER , -- HSP number
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bit-score REAL , -- score (in bits) of HSP
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score REAL , -- score of HSP
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evalue REAL , -- e-value of HSP
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query-from INTEGER , -- start of HSP in query
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query-to INTEGER , -- end of HSP
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hit-from INTEGER, -- start of HSP in subject
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hit-to INTEGER , -- end of HSP in subject
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pattern-from INTEGER OPTIONAL , -- start of PHI-BLAST pattern
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pattern-to INTEGER OPTIONAL , -- end of PHI-BLAST pattern
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query-frame INTEGER OPTIONAL , -- translation frame of query
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hit-frame INTEGER OPTIONAL , -- translation frame of subject
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identity INTEGER OPTIONAL , -- number of identities in HSP
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positive INTEGER OPTIONAL , -- number of positives in HSP
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gaps INTEGER OPTIONAL , -- number of gaps in HSP
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align-len INTEGER OPTIONAL , -- length of the alignment used
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density INTEGER OPTIONAL , -- score density
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qseq VisibleString , -- alignment string for the query (with gaps)
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hseq VisibleString, -- alignment string for subject (with gaps)
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midline VisibleString OPTIONAL -- formating middle line
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}
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END
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