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blastread

Read data from NCBI BLAST report file

Syntax

Data = blastread(BLASTReport)

Input Arguments

BLASTReport

NCBI BLAST-formatted report specified by any of the following:

  • File name or path and file name, such as returned by the getblast function with the 'ToFile' property.

  • URL pointing to an NCBI BLAST report.

  • MATLAB® character array that contains the text for an NCBI BLAST report.

If you specify only a file name, that file must be on the MATLAB search path or in the MATLAB Current Folder.

Output Arguments

DataMATLAB structure or array of structures (if multiple query sequences) containing fields corresponding to BLAST keywords and data from an NCBI BLAST report.

Description

The Basic Local Alignment Search Tool (BLAST) offers a fast and powerful comparative analysis of protein and nucleotide sequences against known sequences in online databases. BLAST reports can be lengthy, and parsing the data from the various formats can be cumbersome.

Data = blastread(BLASTReport) reads a BLAST report from BLASTReport, an NCBI-formatted report, and returns Data, a MATLAB structure or array of structures (if multiple query sequences) containing fields corresponding to the BLAST keywords. blastread parses the basic BLAST reports BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX.

Data contains the following fields.

FieldDescription
RIDRequest ID for retrieving results for a specific NCBI BLAST search.
AlgorithmNCBI algorithm used to do a BLAST search.
QueryIdentifier of the query sequence submitted to a BLAST search.
DatabaseAll databases searched.
Hits.NameName of a database sequence (subject sequence) that matched the query sequence.
Hits.LengthLength of a subject sequence.
Hits.HSPs.ScorePairwise alignment score for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.ExpectExpectation value for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.IdentitiesIdentities (match, possible, and percent) for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.Positives Identical or similar residues (match, possible, and percent) for a high-scoring sequence pair between the query sequence and a subject amino acid sequence.

    Note:   This field applies only to translated nucleotide or amino acid query sequences and/or databases.

Hits.HSPs.Gaps Nonaligned residues (match, possible, and percent) for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.FrameReading frame of the translated nucleotide sequence for a high-scoring sequence pair between the query sequence and a subject sequence.

    Note:   This field applies only when performing translated searches, that is, when using tblastx, tblastn, and blastx.

Hits.HSPs.Strand Sense (Plus = 5' to 3' and Minus = 3' to 5') of the DNA strands for a high-scoring sequence pair between the query sequence and a subject sequence.

    Note:   This field applies only when using a nucleotide query sequence and database.

Hits.HSPs.Alignment Three-row matrix showing the alignment for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.QueryIndicesIndices of the query sequence residue positions for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.SubjectIndicesIndices of the subject sequence residue positions for a high-scoring sequence pair between the query sequence and a subject sequence.
StatisticsSummary of statistical details about the performed search, such as lambda values, gap penalties, number of sequences searched, and number of hits.

Examples

  1. Create an NCBI BLAST report request using a GenPept accession number.

    RID = blastncbi('AAA59174', 'blastp', 'expect', 1e-10)
    
    RID = 
    
        '1175088155-31624-126008617054.BLASTQ3'
  2. Pass the Request ID for the report to the getblast function, and save the report data to a text file.

    getblast(RID, 'ToFile' ,'AAA59174_BLAST.rpt');

      Note:   You may need to wait for the report to become available on the NCBI Web site before you can run the preceding command.

  3. Using the saved file, read the results into a MATLAB structure.

    resultsStruct = blastread('AAA59174_BLAST.rpt')
    
    resultsStruct = 
    
               RID: '1175093446-29831-201366571074.BLASTQ2'
         Algorithm: 'BLASTP 2.2.16 [Mar-11-2007]'
             Query: [1x63 char]
          Database: [1x96 char]
              Hits: [1x50 struct]
        Statistics: [1x1034 char]

References

[1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

[2] Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

For more information about reading and interpreting NCBI BLAST reports, see:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs

See Also

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