(To be removed) Perform search on local BLAST database to create BLAST report
blastlocal will be removed in a future release.
blastlocal('InputQuery', InputQueryValue)
Data = blastlocal('InputQuery', InputQueryValue)
... blastlocal(..., 'Program', ProgramValue,
...)
... blastlocal(..., 'Database', DatabaseValue,
...)
... blastlocal(..., 'BlastPath', BlastPathValue,
...)
... blastlocal(..., 'Expect', ExpectValue,
...)
... blastlocal(..., 'Format', FormatValue,
...)
... blastlocal(..., 'ToFile', ToFileValue,
...)
... blastlocal(..., 'Filter', FilterValue,
...)
... blastlocal(..., 'GapOpen', GapOpenValue,
...)
... blastlocal(..., 'GapExtend', GapExtendValue,
...)
... blastlocal(..., 'BLASTArgs', BLASTArgsValue,
...)
InputQueryValue | Character vector or string specifying the
file name or path and file name of a FASTA file
containing query nucleotide or amino acid
sequence(s). (This corresponds to the
blastall option
-i.) |
ProgramValue | Character vector or string specifying a BLAST program. Choices are:
(The
|
DatabaseValue | Character vector or string specifying a file
name or path and file name of a local BLAST
database (formatted using the NCBI
formatdb function) to search.
Default is a local version of the
nr database in the MATLAB® current folder. (This corresponds to
the blastall option
-d.) |
BlastPathValue | Character vector or string specifying the
full path to the blastall
executable file, including the name and extension
of the executable file. Default is the system
path. |
ExpectValue | Value specifying the statistical significance
threshold for matches against database sequences.
Choices are any real number. Default is
10. (This corresponds to the
blastall option
-e.) |
FormatValue | Integer specifying the alignment format of the BLAST search results. Choices are:
(This corresponds to the
|
ToFileValue | Character vector or string specifying a file
name or path and file name in which to save the
contents of the BLAST report. (This corresponds to
the blastall option
-o.) |
FilterValue | Controls the application of a filter (DUST
filter for the blastn program or SEG filter for
other programs) to the query sequence(s). Choices
are true (default) or
false. (This corresponds to the
blastall option
-F.) |
GapOpenValue | Integer that specifies the penalty for
opening a gap in the alignment of sequences.
Default is -1. (This
corresponds to the blastall
option -G.) |
GapExtendValue | Integer that specifies the penalty for
extending a gap in the alignment of sequences.
Default is -1. (This
corresponds to the blastall
option -E.) |
BLASTArgsValue | NCBI blastall command,
that is a character vector or string containing
one or more instances of
-
and the option associated with it, used to specify
input 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. |
Warning
blastlocal is not supported for macOS version 10.15 (Catalina) or later.
The Basic Local Alignment Search Tool (BLAST) offers a fast and powerful comparative analysis of protein and nucleotide sequences against known sequences in online or local databases.
Note
To use the blastlocal function, you must have a
local copy of the NCBI blastall executable file
(version 2.2.17) available from your system. Run the
downloaded executable and configure it for your system. For
convenience, consider placing the NCBI blastall
executable file on your system path.
blastlocal('InputQuery',
submits query sequence(s) specified by
InputQueryValue)InputQueryValue, a FASTA file containing
nucleotide or amino acid sequence(s), for a BLAST search of a local BLAST
database, by calling a local version of the NCBI blastall
executable file. The BLAST search results are displayed in the MATLAB Command Window. (This corresponds to the
blastall option -i.)
Data = blastlocal('InputQuery', InputQueryValue)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.
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
|
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. |
... blastlocal(..., '
calls PropertyName',
PropertyValue, ...)blastlocal with optional properties that use
property name/property value pairs. You can specify one or more properties
in any order. Each PropertyName must be enclosed
in single quotation marks and is case insensitive. These property
name/property value pairs are as follows.
... blastlocal(..., 'Program',
specifies the BLAST program. Choices are ProgramValue,
...)'blastp'
(default), 'blastn', 'blastx',
'tblastn', and 'tblastx'.
(This corresponds to the blastall option
-p.) For help in selecting an appropriate BLAST
program, visit:
... blastlocal(..., 'Database',
specifies the local BLAST database (formatted using the NCBI
DatabaseValue,
...)formatdb function) to search. Default is a local
version of the nr database in the MATLAB current folder. (This corresponds to the
blastall option -d.)
... blastlocal(..., 'BlastPath',
specifies the full path to the BlastPathValue,
...)blastall executable file,
including the name and extension of the executable file. Default is the
system path.
... blastlocal(..., 'Expect',
specifies a statistical significance threshold for matches against database
sequences. Choices are any real number. Default is ExpectValue,
...)10.
(This corresponds to the blastall option
-e.) You can learn more about the statistics of
local sequence comparison at:
... blastlocal(..., 'Format',
specifies the alignment format of the BLAST search results. Choices
are:FormatValue,
...)
0 (default) — 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
(This corresponds to the blastall option
-m.)
... blastlocal(..., 'ToFile',
saves the contents of the BLAST report to the specified file. (This
corresponds to the ToFileValue,
...)blastall option
-o.)
... blastlocal(..., 'Filter',
specifies whether a filter (DUST filter for the blastn program or SEG filter
for other programs) is applied to the query sequence(s). Choices are
FilterValue,
...)true (default) or false. (This
corresponds to the blastall option
-F.)
... blastlocal(..., 'GapOpen',
specifies the penalty for opening a gap in the alignment of sequences.
Default is GapOpenValue,
...)-1. (This corresponds to the
blastall option -G.)
... blastlocal(..., 'GapExtend',
specifies the penalty for extending a gap in the alignment of sequences.
Default is GapExtendValue,
...)-1. (This corresponds to the
blastall option -E.)
... blastlocal(..., 'BLASTArgs',
specifies options using the input arguments for the NCBI
BLASTArgsValue,
...)blastall function.
BLASTArgsValue is a character vector or
string containing one or more instances or
- and the
option associated with it. For example, to specify the xBLOSUM
45 matrix, you would use the following syntax:
blastlocal('InputQuery', ecoliquery.txt, 'BLASTArgs', '-M BLOSUM45')Tip
Use the 'BlastArgs' property to specify
blastall options for which there are no
corresponding property name/property value pairs.
Note
For a complete list of valid input arguments for the NCBI
blastall function, make sure that the
blastall executable file is located on
your system path or current folder, then type the following at your
system's command prompt.
blastall -
You can also use the syntax and input arguments accepted by the NCBI
blastall function, instead of the
property name/property value pairs listed previously. To do so,
supply a character vector or string containing multiple options
using the -
xoption syntax. For example, you can
specify the ecoliquery.txt FASTA file as your
query sequences, the blastp program, and the
ecoli local database, by using
blastlocal('-i ecoliquery.txt -p blastp -d ecoli')Note
For a complete list of valid input arguments for the NCBI
blastall function, make sure that
the blastall executable file is located
on your system path or current folder, then type the
following at your system's command prompt.
blastall -
[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.