BLIMPS (BLocks IMProved Searcher)
(C) Copyright 1993-1999, Fred Hutchinson Cancer Research Center

README -- General information for BLIMPS


Background:
^^^^^^^^^^
BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a
sequence against blocks or a block against sequences.  BLIMPS augments
the block functions of PATMAT for UNIX, which is no longer supported
by FHCRC. PATMAT for DOS is still available from FHCRC by
anonymous ftp from the NCBI repository (ncbi.nlm.nih.gov/repository/blocks).


Availability:
^^^^^^^^^^^^
BLIMPS is available for anonymous ftp from ncbi.nlm.nih.gov in the
/repository/blocks/unix/blimps/ directory.  BLIMPS is distributed as a
compressed tar file;  be sure to transfer the file in binary mode.

You don't need to have your own copy of BLIMPS to search the
Blocks Database;  BLIMPS is set up as part of the BLOCKS e-mail
server.  Mail to blocks@muller.fhcrc.org with the subject line of
"help" to find out more about the BLOCKS e-mail server.
You can also search the Blocks Database via the World Wide Web,
	http://blocks.fhcrc.org/

The current release of the Blocks Database is available by anonymous
ftp from ncbi.nlm.nih.gov in the /repository/blocks/unix/ directory.


Papers:
^^^^^^
These are just the basic references to get you started.  
See also:	 http://blocks.fhcrc.org/papers/

For the BLOCKS e-mail and WWW servers see:
Steven Henikoff & Jorja G. Henikoff, "Protein family classification
based on searching a database of blocks", Genomics 19:97-107 (1994).

For the BLIMPS searching algorithm see:
J.C. Wallace and S. Henikoff, "PATMAT: a searching and extraction
program for sequence, pattern and block queries and databases",
CABIOS, 8:3, p. 249-254 (1992).

For the Blocks Database see:
Steven Henikoff & Jorja G. Henikoff, "Automated assembly of protein
blocks for database searching", Nucleic Acids Research, 19:23, 
p. 6565-6572. (1991)


Ftp sources for code:
^^^^^^^^^^^^^^^^^^^^
BLIMPS:
ncbi.nlm.nih.gov:/repository/blocks/unix/blimps/

Skiplist package used in BLIMPS:
The skiplist package was written by Dominic Giampaolo <nick@maxine.wpi.edu>. 
homeboy.wpi.edu:/pub/skiplist.tar.Z
Skiplist reference:
William Pugh, "Skip lists: a probabilistic alternative to balanced trees.",
Communications of the ACM.  vol.33, no.6.  pp. 668-76.  June 1990.
<pugh@cs.umd.edu>


BLAST header files used in BLIMPS:
The following header files were written by the authors of BLAST:
ncbi.nlm.nih.gov:/pub/blast/explode/include/aabet.h
ncbi.nlm.nih.gov:/pub/blast/explode/include/alphabet.h
ncbi.nlm.nih.gov:/pub/blast/explode/include/blastapp.h
ncbi.nlm.nih.gov:/pub/blast/explode/include/gcode.h
ncbi.nlm.nih.gov:/pub/blast/explode/include/ntbet.h
ncbi.nlm.nih.gov:/pub/blast/explode/lib/gcode.c
BLAST reference:
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and
David J. Lipman (1990).  A basic local alignment search tool.
J. Mol. Biol. 215:403-410.

Note that the original code in the skiplists and the BLAST header files
has been modified for BLIMPS.

BLIMPS was written by Bill Alford, who is currently a World Wide Web 
developer at the Fred Hutchinson Cancer Research Center: balford@fhcrc.org

----------------------------------------------------------------------
For BLIMPS questions, please contact:
Jorja Henikoff 					jorja@fhcrc.org
Fred Hutchinson Cancer Research Center  	FAX: 206-667-5889
1100 Fairview AV N, A1-162, PO Box 19024   	Seattle, WA 98109-1024
