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

Perform BLAST search

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

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

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

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.

Version History

Introduced before R2006a