blastdata = getblast(RID)
retrieves RID, the Request ID for the NCBI BLAST report, and
returns the report data in blastdata, a MATLAB® structure. The Request ID, RID, must be recent
because NCBI purges reports after 36 hours.
blastdata = getblast(RID,Name,Value)
uses additional options specified by one or more name-value pair arguments.
Perform a BLAST search on a protein sequence and save the results to an XML file.
Get a sequence from the Protein Data Bank and create a MATLAB structure.
S = getpdb('1CIV');
Use the structure as input for the BLAST search with a significance threshold of 1e-10. The first output is the request ID, and the second output is the estimated time (in minutes) until the search is completed.
Get the search results from the report. You can save the XML-formatted report to a file for an offline access. Use ROTE as the wait time to retrieve the results.
RID — Request ID for NCBI BLAST search character vector | string
Request ID for retrieving results from a specific NCBI BLAST search,
specified as a character vector or string.
Example: 'GTF033EZ015'
Name-Value Pair Arguments
Specify optional
comma-separated pairs of Name,Value arguments. Name is
the argument name and Value is the corresponding value.
Name must appear inside quotes. You can specify several name and value
pair arguments in any order as
Name1,Value1,...,NameN,ValueN.
Example: 'ToFile','report.xml' saves the results to a file named
report.xml.
'ToFile' — Name of file to save report data to character vector | string
Name of the file to save the report data to, specified as the
comma-separated pair consisting of 'ToFile' and a
character vector or string. The file is XML-formatted by default.
Example: 'ToFile','Report.xml'
'WaitTime' — Time to wait for report 0 (default) | nonnegative integer
Time (in minutes) to wait for the report from NCBI to be ready,
specified as the comma-separated pair consisting of
'WaitTime' and a nonnegative integer. If the
report is still not ready after the specified time, an error is
generated.
The default value is 0, that is, there is no delay in retrieving the
report.
Tip
Use the RTOE, request time of execution,
returned by the blastncbi
function as the wait time here.
ID of the subject sequence that matched the query sequence
Definition
Description of the subject sequence
Accession
Accession of the subject sequence
Length
Length of the subject sequence
Hsps
Structure containing Information on the
high-scoring segment pairs (HSPs)
Hits.Hsps
This table summarizes the fields of Hits.Hsps.
Field
Description
Score
Pairwise alignment score for a high-scoring segment pair between the query sequence and a
subject sequence.
BitScore
Bit score for a high-scoring segment pair.
Expect
Expectation value for a high-scoring segment pair.
Identities
Number of identical or similar residues for a high-scoring segment pair between the query
sequence and a subject sequence.
Positives
Number of identical or similar residues for a high-scoring sequence pair between the query
sequence and a subject amino acid sequence. This
field applies only to translated nucleotide or
amino acid query sequences and databases.
Gaps
Nonaligned residues for a high-scoring segment pair.
AlignmentLength
Length of the alignment for a high-scoring segment pair.
QueryIndices
Indices of the query sequence residue positions for a high-scoring segment pair.
SubjectIndices
Indices of the subject sequence residue positions for a high-scoring segment pair.
Frame
Reading frame of the translated nucleotide sequence for a high-scoring segment pair.
Alignment
3-by-N character array showing the alignment for a high-scoring sequence
pair between the query sequence and a subject
sequence. The first row is the query sequence, the
second row is the alignment, and the third row is
the subject sequence.
The 'Alignments' name-value pair has been removed. The number
of hits returned in the output is controlled by the number of hits in the input
BLAST report.
'Descriptions' option has been removed
Errors starting in R2017b
The 'Descriptions' name-value pair has been removed. The number
of hits returned in the output is controlled by the number of hits in the input
BLAST report.
'FileFormat' option has been removed
Errors starting in R2017b
The 'FileFormat' name-value pair has been removed. The file is
XML-formatted automatically.
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