bblast- batch blast search tool available

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Tue Jan 17 17:49:26 EST 1995


BBLAST- BATCH BLAST SEARCH TOOL AVAILABLE
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

WHAT IS BBLAST?
---------------
bblast provides an easy way to query protein and nucleotide local or
remote databases (through the network or email servers at NCBI) using
any of the blast programs and all their supported options.

bblast permits one or many sequences to be searched against one
or many databases using several different BLAST programs. bblast
eliminates the tedious task of manually querying the server for
each individual sequence and presents a user-friendly interface
to searching databases using the blast programs.

Presently bblast supports the following blast (v 1.4) programs:

	 blastn
	 blastp
	 blastx
	tblastn
	tblastx

for searches against all the databases currently maintained at NCBI,
as well as any local databases.


Why use it?
-----------
bblast is an ideal way to perform batch database searches or regular
queries to molecular sequence databases; it can be used interactively
(where the user sets various query parameters) or in batch mode
(where parameters are supplied using command-line switches, options
and arguments).

bblast shields the infrequent or non-power user from many of the 
complexities of performing blast searches.  Where are the databases? 
What databases can I search?  What parameters should I use?  How do
I get the results back?  What if I also have local blast databases to
search?  What if I have a DNA sequence but want to compare it to a
protein sequence database?

In interactive mode, bblast asks the user a series of simple questions
so that the desired sequence(s) can be effortlessly searched against the
appropriate database(s) with the results returned in the way that best
suits the user.  bblast detects the type of sequence used for the query
(nucleotide or protein), asks (for nucleotide) what the _information_
content of both the query sequence and the database are (i.e. the
nucleotide or protein information in a nucleotide sequence).  In this
way the user is shielded from having to deal with the complexities of all
the various blast programs.

In batch mode, bblast can be configured to search databases at the
users' convenience (using deliberately scheduled jobs). For instance you
may want to query the nucleotide daily update databases at NCBI using
tblastx as well as the protein databases using blastp.  This is
particularly useful when daily searches are required (e.g. when you
have a sequence but it does not match anything in the database, you want
to check every day to see if something new has been sequenced that matches
your sequence).


How does it work?
-----------------
bblast processes the input file by first extracting each sequence, and
determining which datasource (local/remote), database (local, or any of
those at NCBI) and method (local, network, email) should be used for the
search.

When the user requests a local or network method, the results are saved in
files in a local directory specified by the user.  If the user performs a
request by email, the results are sent back to the user as mail messages by
the NCBI server.  Either type of results can then be browsed, and sequences
in the databases retrieved, using the tbob program (also available from the
OGMP).

bblast also can use one or many resource files that permit the user to
painlessly configure all possible options to the various blast programs.


System requirements
-------------------
A UNIX system with a perl interpreter installed.


Platforms/Operating Systems
---------------------------
BBLAST requires the following:

   - For email and network searches, a computer on the Internet running UNIX
   - A perl interpreter
   - For network searches, the network blast clients
   - For local database searches, the local blast clients

See the INSTALLATION and getting.perl documents for more information on
installing bblast.


Obtaining BBLAST
----------------
BBLAST can be obtained by gopher by pointing your gopher client at the
following URLs:

    gopher://megasun.bch.umontreal.ca:70/11/CMB/Databases/Blast/bblast

    ftp://megasun.bch.umontreal.ca

(anonymous ftp to megasun.bch.umontreal.ca  Files can be retrieved from
the /pub/bblast directory)


FURTHER INFORMATION
-------------------
For more information about the parboot project, send email to the  
Informatics Division of the Organelle Genome Megasequencing Program
at the Universite de Montreal:
  
        ogmp at bch.umontreal.ca
  
All feedback welcome.
  

ACKNOWLEDGMENTS
---------------
This work was supported in part by the Medical Research Council, Canada
(grant No. SP-34), the Canadian Genome Analysis & Technology program
(grant No. GO-12323) and Sun Microsystems.


AUTHORS
-------
Pierre Rioux,
Tim Littlejohn (Project Management),
Organelle Genome Megasequencing Program, Jan, 1995


-- 
==============================================================================
Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
            C.P. 6128, Centre-ville
            Montreal (Quebec), H3C 3J7
            CANADA
==============================================================================




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