| Bioinformatics Toolbox | |
Get BLAST report from NCBI web site
Data = getblast(RID, 'PropertyName', PropertyValue...) getblast(..., 'Descriptions', DescriptionsValue) getblast(..., 'Alignments', AlignmentsValue) getblast(..., 'ToFile', ToFileValue) getblast(..., 'FileFormat', FileFormatValue)
| RID | BLAST Request ID (RID) from the function blastncbi. |
| Descriptions | |
| Alignments | Property to select the number of alignments in a report. Enter values from 1 to 100. The default value is 50. |
| ToFile | Property to enter a filename for saving report data. |
| FileFormat | Property to select the format of the file named in ToFileValue. Enter either 'TEXT' or 'HTML'.The default value is 'TEXT'. |
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. getblast parses NCBI BLAST reports, including BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX and psi-BLAST.
Data = getblast(RID, 'PropertyName', PropertyValue...) reads a BLAST Request ID (RID) and returns the report data in a structure (Data). The NCBI Request ID (RID) must be a recently generated report because NCBI purges reports after 24 hours.
getblast(..., 'Descriptions', DescriptionsValue) includes the specified number of descriptions (DescriptionsValue) in the report.
getblast(..., 'Alignments', AlignmentsValue) includes the specified number of alignments in the report.
getblast(..., 'ToFile', ToFileValue) saves the data returned from the NCBI BLAST report to a file (ToFileValue). The default format for the file is text, but you can specify HTML with the property FileFormat.
getblast(..., 'FileFormat', FileFormatValue) returns the report in the specified format (FileFormatValue).
For more information about reading and interpreting BLAST reports, see
http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Blast_output.html
Run a BLAST search with an NCBI accession number.
RID = blastncbi('AAA59174','blastp','expect',1e-10)
% Then pass the RID to GETBLAST to parse the report, load it into
% a MATLAB structure, and save a copy as a text file.
report = getblast(RID,'TOFILE','Report.txt')
Bioinformatics Toolbox functions blastncbi, blastread
| | getancestors (biograph) | getbyname (phytree) | |
© 1994-2005 The MathWorks, Inc.