NAME - Bioperl module for running Blast analyses locally.


    use Bio::Tools::Blast::Run::LocalBlast qw(&blast_local);

    &blast_local( %named_parameters);

See blast_local() for a description of available parameters.


This module is included with the central Bioperl distribution:

Follow the installation instructions included in the README file.

DESCRIPTION contains methods and data necessary for running Blast sequence analyses on a local machine. This module must be customized for a specific site.

The basic requirements are that it conform to this minimal API:

1 Export a method called blast_local()

that accepts a object + named parameters as specified by blast_local().

2 The blast_local() method should return

a list of names of files containing the raw Blast reports.

3 Export arrays containing a list of available databases

in the arrays @Blast_dbn_local and @Blast_dbp_local.

The generic version of this module provides some rudimentary logic, but feel free to customize as necessary.

Script Files

Sometimes it is convenient to write an executable shell script for running a set of Blasts on a local machine. This script can be saved and re-executed as necessary or saved for documentation purposes. This module could provide a convenient way to consolidate the logic necessary for producing such script files or perhaps stubs of script file that could be further modified for Blast-ing specific datasets.

DEPENDENCIES is used by The development of this is linked with the module and should be updated along with that module.

SEE ALSO                    - Blast object.   - Script for accessing remote server.     - Utility module for running Blasts remotely.              - Blast HTML-formating utility class.                             - Biosequence object  - Online module documentation        - Bioperl Blast Project                       - Bioperl Project Homepage


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.          - General discussion     - Technically-oriented discussion             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:                         


Steve A. Chervitz,



Copyright (c) 1998 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.


 Usage     : @files = blast_local($blast_object,  %namedParameters);
           : This method is exported.
 Purpose   : Run a local Blast analysis on one or more sequences.
           : This method defines the API for your module.
 Returns   : Array containing a list of filenames of the Blast reports.
 Argument  : $blast_object = object ref for a object.
           : %named parameters: (PARAMETER TAGS CAN BU UPPER OR LOWER CASE)
           : These are some basic parameters. Supply more as desired.
           :   -SEQS       => ref to an array of objects. 
           :   -SEQ_FILES  => ref to an array of strings containing full-path file names.
           :   -PROG       => name of blast program (blastp, blastx, etc.)
           :   -DATABASE   => name of database (see below.)
           :   -EXPECT     => expect value cutoff
           :   -FILTER     => sequence complexity filter ('default' or 'none')
           :   -MATRIX     => substitution scoring matrix (blast1 only for NCBI server)
           :   -DESCR      => integer, number of on-line descriptions (V, 100)
           :   -ALIGN      => integer, number of alignments (B, 100)
           :   -GAP        => 'on' or 'off'
           :   -OUT_DIR    => output directory to store blast result files
 Throws    : Exception if:
           :   - Cannot obtain parameters by calling _rearrange() on the
           :     first argument, which should be a object ref.
           :   - No sequences are provided (objects or files).
           :   - Sequence type is incompatible with Blast program type.
           :   - Database name is not one of the valid names.
 Comments  :
  Available programs: blastn, blastx, blastp, tblastn, tblastx

  Available local databases are: 

    These are exported by this module in the @Blast_dbp_local
    and @Blast_dbn_local arrays.
  Available substitution scoring matrices: 
    (Here are the standard ones)
    BLOSUM: 100,90,85,80,75,70,65,62,60,55,50,45,40,35,30
    PAM:    500,490,480,470,460,450,440,430,420,410,400,390,380,370,360,350

    These are exported by this module in the @Blast_matrix_local
  Available sequence complexity filters:
       SEG, SEG+XNU, XNU, dust, none.

See Also : _set_options(), _validate_options(), _blast_seqs(), _blast_files(),