blastreadlocal - Read data from local BLAST report

Syntax

Input Arguments

BLASTReport

BLAST report specified by any of the following: File name or path and file name of a locally created BLAST report file, such as returned by the blastlocal function with the 'ToFile' property. MATLAB character array that contains the text for a local BLAST report. If you specify only a file name, that file must be on the MATLAB search path or in the current folder.

Format

Integer specifying the alignment format used to create BLASTReport. Choices are: 0 — Pairwise 1 — Query-anchored, showing identities 2 — Query-anchored, no identities 3 — Flat query-anchored, showing identities 4 — Flat query-anchored, no identities 5 — Query-anchored, no identities and blunt ends 6 — Flat query-anchored, no identities and blunt ends 7 — Not used 8 — Tabular 9 — Tabular with comment lines

Output Arguments

Data	MATLAB structure or array of structures (if multiple query sequences) containing fields corresponding to BLAST keywords and data from a local 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 and local databases. BLAST reports can be lengthy, and parsing the data from the various formats can be cumbersome.

Data = blastreadlocal(BLASTReport, Format) reads BLASTReport, a locally created BLAST report file, and returns Data, a MATLAB structure or array of structures (if multiple query sequences) containing fields corresponding to BLAST keywords and data from a local BLAST report. Format is an integer specifying the alignment format used to create BLASTReport.

Note   The function assumes the BLAST report was produced using version 2.2.17 of the blastall executable.

Data contains a subset of the following fields, based on the specified alignment format.

Field	Description
Algorithm	NCBI algorithm used to do a BLAST search.
Query	Identifier of the query sequence submitted to a BLAST search.
Length	Length of the query sequence.
Database	All databases searched.
Hits.Name	Name of a database sequence (subject sequence) that matched the query sequence.
Hits.Score	Alignment score between the query sequence and the subject sequence.
Hits.Expect	Expectation value for the alignment between the query sequence and the subject sequence.
Hits.Length	Length of a subject sequence.
Hits.HSPs.Score	Pairwise alignment score for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.Expect	Expectation value for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.Identities	Identities (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.Mismatches	Residues that are not similar to each other (match, possible, and percent) for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.Frame	Reading 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.QueryIndices	Indices of the query sequence residue positions for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.SubjectIndices	Indices of the subject sequence residue positions for a high-scoring sequence pair between the query sequence and a subject sequence.
Hits.HSPs.AlignmentLength	Length of the pairwise alignment for a high-scoring sequence pair between the query sequence and a subject sequence.
Alignment	Entire alignment for the query sequence and the subject sequence(s).
Statistics	Summary of statistical details about the performed search, such as lambda values, gap penalties, number of sequences searched, and number of hits.

Examples

The following examples assume you have a FASTA nucleotide file for E. coli, such as the file NC_004431.fna, which you can download from ftp://ftp.ncbi.nih.gov/genomes/Bacteria/, saved to your MATLAB current folder.

Reading Data Using a Tabular Alignment Format

1. Create a local blastable database from the NC_004431.fna FASTA file.

   blastformat('inputdb', 'NC_004431.fna', 'protein', 'false');

2. Use the getgenbank function to retrieve two sequences from the GenBank database.

   S1 = getgenbank('M28570.1');
   S2 = getgenbank('M12565');

3. Create a query file by using the fastawrite function to create a FASTA file named query_multi_nt.fa from these two sequences, using the only accession number as the header.

   Seqs(1).Header = S1.Accession;
   Seqs(1).Sequence = S1.Sequence;
   Seqs(2).Header = S2.Accession;
   Seqs(2).Sequence = S2.Sequence;
   fastawrite('query_multi_nt.fa', Seqs);

4. Submit the query sequences in the query_multi_nt.fa FASTA file for a BLAST search of the local nucleotide database NC_004431.fna. Specify the BLAST program blastn and a tabular alignment format. Save the contents of the BLAST report to a file named myecoli_nt8.txt, and then read the local BLAST report.

   blastlocal('inputquery', 'query_multi_nt.fa',...
              'database', 'NC_004431.fna',...
              'tofile', 'myecoli_nt8.txt', 'program', 'blastn',...
              'format', 8);
   blastreadlocal('myecoli_nt8.txt', 8);
   

Reading Data Using a Query Anchored Format

1. If you have not already done so, create a local blastable database and a query file as described in steps 1 through 3 in Reading Data Using a Tabular Alignment Format.

2. Submit the query sequences in the query_multi_nt.fa FASTA file for a BLAST search of the local nucleotide database NC_004431.fna. Specify the BLAST program blastn and a query-anchored format. Save the contents of the BLAST report to a file named myecoli_nt1.txt, and then read the local BLAST report, saving the results in results, an array of structures.

   blastlocal('inputquery', 'query_multi_nt.fa',...
              'database', 'NC_004431.fna',...
              'tofile', 'myecoli_nt1.txt', 'program', 'blastn',...
              'format', 1);
   results = blastreadlocal('myecoli_nt1.txt', 1);
   

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 BLAST reports, see:

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

See Also

blastformat | blastlocal | blastncbi | blastread | getblast

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