131 lines
5.0 KiB
Groff
131 lines
5.0 KiB
Groff
NCBI-BlastOutput2 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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BlastOutput2 ::= SEQUENCE {
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report Report OPTIONAL,
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error Err OPTIONAL
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}
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BlastXML2 ::= SET OF BlastOutput2
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Report ::= 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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search-target Target,
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params Parameters, -- search parameters
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results Results
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}
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Err ::= SEQUENCE {
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code INTEGER,
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message VisibleString OPTIONAL
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}
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Target ::= CHOICE {
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db VisibleString , -- BLAST Database name
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subjects SEQUENCE OF VisibleString -- Subject IDs
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}
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Results ::=CHOICE {
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iterations SEQUENCE OF Iteration ,
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-- iterative search (psi and delta blast)
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search Search, -- db search
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bl2seq SEQUENCE OF Search -- bl2seq
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}
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Iteration ::= SEQUENCE {
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iter-num INTEGER, -- iteration number (use with psiblast)
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search Search
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}
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Search ::= SEQUENCE {
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query-id VisibleString OPTIONAL, -- SeqId of query
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query-title VisibleString OPTIONAL, -- Definition line of query
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query-len INTEGER OPTIONAL , -- length of query sequence
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query-masking SEQUENCE OF Range OPTIONAL, -- Masked offsets.
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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 OPTIONAL, -- Gap opening cost (-G)
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gap-extend INTEGER OPTIONAL, -- 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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cbs INTEGER OPTIONAL, -- composition-based stats (numbers correspond to
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-- numbering in stand-alone application parameter -comp_based_stats).
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query-gencode INTEGER OPTIONAL, -- genetic code for query (blastx or tblastx)
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db-gencode INTEGER OPTIONAL, -- genetic code for db or subjects (tblastn or tblastx)
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bl2seq-mode VisibleString OPTIONAL -- bl2seq mode
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}
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-- Used to specify start/stop of masking on query.
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Range ::= SEQUENCE {
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from INTEGER, -- Beginning of masked range (one-offset)
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to INTEGER -- End of masked range (one-offset)
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}
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Statistics ::= SEQUENCE {
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db-num BigInt OPTIONAL, -- Number of sequences in BLAST db
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db-len BigInt OPTIONAL, -- Length of BLAST db
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hsp-len INTEGER , -- Effective HSP length
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eff-space BigInt, -- 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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-- Description of entries for this (possibly non-redundant) sequence.
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HitDescr ::= SEQUENCE {
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id VisibleString , -- SeqId of subject
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accession VisibleString OPTIONAL, -- accession
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title VisibleString OPTIONAL, -- title (definition line) of subject
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taxid INTEGER OPTIONAL, -- NCBI taxid (9606 for human)
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sciname VisibleString OPTIONAL -- binomial scientific name ("Homo sapiens" for human).
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}
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Hit ::= SEQUENCE {
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num INTEGER , -- hit number
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description SEQUENCE OF HitDescr, -- ID, title, and taxonomy for each entry in the PIG
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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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identity INTEGER OPTIONAL , -- number of identities in HSP
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positive INTEGER OPTIONAL , -- number of positives in HSP
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density INTEGER OPTIONAL , -- score density
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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-from INTEGER , -- start of HSP in query
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query-to INTEGER , -- end of HSP
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query-strand VisibleString OPTIONAL, -- Strand of query (blastn)
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query-frame INTEGER OPTIONAL , -- translation frame of query (blastx, tblastx)
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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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hit-strand VisibleString OPTIONAL, -- Strand of subject (blastn)
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hit-frame INTEGER OPTIONAL , -- translation frame of subject (tblastn, tblastx)
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align-len INTEGER OPTIONAL , -- length of the alignment used
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gaps INTEGER OPTIONAL , -- number of gaps in HSP
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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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