blastread

Read data from NCBI BLAST report file

Syntax

blastdata = blastread(blastreport)

Description

blastdata = blastread(blastreport) reads the NCBI BLAST report data from an XML-formatted file, blastreport, and returns blastdata, a structure containing the corresponding BLAST data.

Examples

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Perform BLAST search

Open Script

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.

[RID1,ROTE] = blastncbi(S,'blastp','expect',1e-10);

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.

report1 = getblast(RID1,'WaitTime',ROTE,'ToFile','1CIV_report.xml')

Blast results are not available yet. Please wait ...

report1 = 

  struct with fields:

                RID: 'R49TJMCF014'
          Algorithm: 'BLASTP 2.6.1+'
           Database: 'nr'
            QueryID: 'Query_224139'
    QueryDefinition: 'unnamed protein product'
               Hits: [1×100 struct]
         Parameters: [1×1 struct]
         Statistics: [1×1 struct]

Use blastread to read BLAST data from the XML-formatted BLAST report file.

blastdata = blastread('1CIV_report.xml')

blastdata = 

  struct with fields:

                RID: ''
          Algorithm: 'BLASTP 2.6.1+'
           Database: 'nr'
            QueryID: 'Query_224139'
    QueryDefinition: 'unnamed protein product'
               Hits: [1×100 struct]
         Parameters: [1×1 struct]
         Statistics: [1×1 struct]

Alternatively, run the BLAST search with an NCBI accession number.

RID2 = blastncbi('AAA59174','blastp','expect',1e-10)

RID2 =

    'R49WAPMH014'

Get the search results from the report.

report2 = getblast(RID2)

Blast results are not available yet. Please wait ...

report2 = 

  struct with fields:

                RID: 'R49WAPMH014'
          Algorithm: 'BLASTP 2.6.1+'
           Database: 'nr'
            QueryID: 'AAA59174.1'
    QueryDefinition: 'insulin receptor precursor [Homo sapiens]'
               Hits: [1×100 struct]
         Parameters: [1×1 struct]
         Statistics: [1×1 struct]

Input Arguments

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`blastreport` — Name of BLAST report file
character vector | string

Name of an XML-formatted BLAST report file, specified as a character vector or string.

Example: 'blastreport.xml'

Output Arguments

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`blastdata` — BLAST report data
structure

BLAST report data, returned as a structure that contains the following fields:

Field	Description
`RID`	Request ID for retrieving results from a specific NCBI BLAST search
`Algorithm`	NCBI algorithm used to perform the BLAST search
`Database`	All databases searched
`QueryID`	Identifier of the query sequence
`QueryDefinition`	Definition of the query sequence
`Hits`	Structure containing information on the hit sequences, such as IDs, accession numbers, lengths, and HSPs (high-scoring segment pairs)
`Parameters`	Structure containing information on the input parameters used to perform the search
`Statistics`	Summary of statistical details about the performed search, such as lambda, kappa, and entropy values

More About

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Hits

This table lists each field of blastdata.Hits.

Field	Description
`ID`	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.