Codebase list libnhgri-blastall-perl / HEAD
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Send bug reports to webblaster@nhgri.nih.gov

See Changes file for revision history.

---------------------------------------------------------------------------
Warning:  The parsing methods have been tested against GenBANK datasets.
          If you are using private databases that have non-standard
          deflines, you will want to adjust the defline id regex.
          See DB_ID_REGEX section of the pod documentation
          There is also a testing script to help develop a regular expression
          that fits your databases.  Look in the scripts subdirectory of
          the distribution.
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If you have NCBI's BLAST2 or WU-BLAST installed locally and your
environment is already setup you can use Perl's object-oriented
capabilities to run your BLASTs.  Also if you have a blastcl3 binary
from the toolkit (or binaries from our FTP site) you can run BLAST over 
the network.  There are also methods to blast single sequences against
each other using the bl2seq binaries (also in the toolkit and binaries).
You can blast one sequence against a library of sequences using the
blast_one_to_many method.  You can format databases with formatdb method.
You can also have NHGRI::Blastall read existing BLAST 
reports.  If you have a database of repetitive DNA or other DNA you would
like to mask out, you can use the mask method to mask the data against 
these databases. You can then use either the filter or result methods 
to parse the report and access the various elements of the data.

If you need help installing NCBI's local blast check... 

    http://genome.nhgri.nih.gov/blastall/blast_install/

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IT IS HIGHLY RECOMMENDED THAT YOU READ THROUGH THE POD DOCUMENTATION
embedded in the module to learn how to use NHGRI::Blastall.  
It won't take you that long.  After Installation...

    perldoc NHGRI::Blastall

the on-line manual page is available at 

    http://genome.nhgri.nih.gov/blastall/Blastall.html

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If you have problems, questions, comments send to webblaster@nhgri.nih.gov

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PUBLIC DOMAIN NOTICE

This software/database is ``United States Government Work'' under the 
terms of the United States Copyright Act. It was written as part of 
the authors' official duties for the United States Government and thus 
cannot be copyrighted. This software/database is freely available to 
the public for use without a copyright notice. Restrictions cannot 
be placed on its present or future use. 

Although all reasonable efforts have been taken to ensure the accuracy 
and reliability of the software and data, the National Human Genome 
Research Institute (NHGRI) and the U.S. Government does not and cannot 
warrant the performance or results that may be obtained by using this 
software or data.  NHGRI and the U.S. Government disclaims all 
warranties as to performance, merchantability or fitness for any 
particular purpose. 

In any work or product derived from this material, proper attribution 
of the authors as the source of the software or data should be made, 
using http://genome.nhgri.nih.gov/webblast as the citation. 

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Special thanks to Peter Chines for reporting a bunch of bugs and suggesting
some excellent features.

Thanks to David Lapointe from UMass Medical School for his suggestion 
to use blastcl3 for network blasting.

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