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blastread

Read data from NCBI BLAST report file

Syntax 

Data = blastread(File)

Arguments

File

NCBI BLAST formatted report file. Enter a filename, a path and filename, or a URL pointing to a file. File can also be a MATLAB character array that contains the text for a NCBI BLAST report.

Description

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

Data = blastread(File) reads a BLAST report from an NCBI formatted file (File) and returns a data structure (Data) containing fields corresponding to the BLAST keywords.

Data contains the following fields

RID 
Algorithm 
Query 
Database 
Hit.Name 
Hit.Length 
Hit.HSP.Score 
Hit.HSP.Expect 
Hit.HSP.Identities 
Hit.HSP.Positives  (peptide sequences) 
Hit.HSP.Gaps 
Hit.HSP.Frame      (translated searches) 
Hit.HSP.Strand     (nucleotide sequences)

blastread parses the basic BLAST reports BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX.

For more information about reading and interpreting BLAST reports, see 

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Blast_output.html

Examples

% Create a BLAST request with a GenPept accession number. 
RID = blastncbi('AAA59174', 'blastp', 'expect', 1e-10) 
% 
% Then pass the RID to getblast to download the report and save
% it to a text file. 
getblast(RID, 'ToFile' ,'AAA59174_BLAST.rpt') 

% Using the saved file, read the results into a MATLAB structure. 
results = blastread('AAA59174_BLAST.rpt')

See Also

Bioinformatics Toolbox functions blastncbi, getblast

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