Bioinformatics Toolbox™

blastformat - Create local BLAST database

Syntax

blastformat('Inputdb', InputdbValue)

blastformat(..., 'FormatPath', FormatPathValue, ...)
blastformat(..., 'Title', TitleValue, ...)
blastformat(..., 'Log', LogValue, ...)
blastformat(..., 'Protein', ProteinValue, ...)
blastformat(..., 'FormatArgs', FormatArgsValue, ...)

Arguments

Description

Note   To use the blastformat function, you must have a local copy of the NCBI formatdb executable file available from your system. You can download the formatdb executable file by accessing http://www.ncbi.nlm.nih.gov/blast/download.shtml then clicking the download link under the blast column for your platform. Run the downloaded executable and configure it for your system. For more information, see the readme file on the NCBI ftp site at: ftp://ftp.ncbi.nih.gov/blast/documents/blast.html For convenience, consider placing the NCBI formatdb executable file on your system path.

blastformat('Inputdb', InputdbValue) calls a local version of the NCBI formatdb executable file with InputdbValue, a file name or path and file name of a FASTA file containing a set of sequences. If you specify only a file name, that file must be on the MATLAB search path or in the current directory. (This corresponds to the formatdb option -i.)

It then formats the sequences as a local, blastable database, by creating multiple files, each with the same name as the InputdbValue FASTA file, but with different extensions. The database files are placed in the same location as the FASTA file.

Note   If you rename the database files, make sure they all have the same name.

blastformat(..., 'PropertyName', PropertyValue, ...) calls blastformat 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.

blastformat(..., 'FormatPath', FormatPathValue, ...) specifies the full path to the formatdb executable file, including the name and extension of the executable file. Default is the system path.

blastformat(..., 'Title', TitleValue, ...) specifies the title for the local database. Default is the input FASTA file name. (This corresponds to the formatdb option -t.)

Note   The 'Title' property does not change the file name of the database files. This title is used internally only, and appears in the report structure returned by the blastlocal function.

blastformat(..., 'Log', LogValue, ...) specifies the file name or path and file name for the log file associated with the local database. Default is formatdb.log. The log file captures the progress of the database creation and formatting. (This corresponds to the formatdb option -l.)

blastformat(..., 'Protein', ProteinValue, ...) specifies whether the sequences formatted as a local BLAST database are protein or not. Choices are true (default) or false. (This corresponds to the formatdb option -p.)

blastformat(..., 'FormatArgs', FormatArgsValue, ...) specifies options using the input arguments for the NCBI formatdb function. FormatArgsValue is a string containing one or more instances of -x and the option associated with it. For example, to specify that the input is a database in ASN.1 format, instead of a FASTA file, you would use the following syntax:

blastformat('Inputdb', 'ecoli.asn', 'FormatArgs', '-a T')

Tip   Use the 'FormatArgs' property to specify formatdb options for which there are no corresponding property name/property value pairs.

Note   For a complete list of valid input arguments for the NCBI formatdb function, make sure that the formatdb executable file is located on your system path or current directory, then type the following at your system's command prompt. formatdb -

Using formatdb Syntax

You can also use the syntax and input arguments accepted by the NCBI formatdb function, instead of the property name/property value pairs listed previously. To do so, supply a single string containing multiple options using the -x option syntax. For example, you can specify the ecoli.nt FASTA file, a title of myecoli, and that the sequences are not protein by using

blastformat('-i ecoli.nt -t myecoli -p F')

Note   For a complete list of valid input arguments for the NCBI formatdb function, make sure that the formatdb executable file is located on your system path or current directory, then type the following at your system's command prompt. formatdb -

Examples

Using blastformat with Property Name/Value Pairs

1. Download the ecoli.nt.gz zip file from

   ftp://ftp.ncbi.nih.gov/blast/db/FASTA/

   and then extract the ecoli.nt FASTA file to your MATLAB current directory.

2. Create a local blastable database from the ecoli.nt FASTA file and give it a title using the 'title' property.

   blastformat('inputdb', 'ecoli.nt', 'protein', 'false',...
               'title', 'myecoli_nt');

Using blastformat with formatdb Syntax and Input Arguments

1. Download the ecoli.aa.gz zip file from

   ftp://ftp.ncbi.nih.gov/blast/db/FASTA/

   and then extract the ecoli.aa FASTA file to your MATLAB current directory.

2. Create a local blastable database from the ecoli.aa FASTA file and rename the title and log file using formatdb syntax and input arguments.

   blastformat('inputdb', 'ecoli.aa',...
               'formatargs', '-t myecoli_aa -l ecoli_aa.log');

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 on the NCBI formatdb function, see:

http://www.ncbi.nlm.nih.gov/blast/docs/formatdb.html

See Also

Bioinformatics Toolbox™ functions: blastlocal, blastncbi, blastread, blastreadlocal, getblast

biograph

blastlocal