Subject: Re: Information on submissions
From: Jorja Henikoff <[email-masked]>
To: [email-masked]
Date: Wed, 21 Jul 1999 11:12:55 -0700 (PDT)

7/21/99	Fly Annotation Experiment - BLOCKS

-----------------------------------------------------------------------------
1. List of credits:

Jorja & Steven Henikoff 		           [email-masked]
Fred Hutchinson Cancer Research Center  	   FAX: 206-667-5889
1100 Fairview AV N, A1-162, PO Box 19024  	   Seattle, WA 98109-1024
http://blocks.fhcrc.org

-----------------------------------------------------------------------------
2. Short method:

Searched 2.9mb DNA sequence vs Blocks+ (15June99, http://blocks.fhcrc.org)
and vs blocks extracted from Smart 3.0 multiple alignments 
(http://coot-embl-heidelberg.de/SMART/) using BLIMPS, which translates
the DNA sequence in all 6 frames for comparison with blocks.
Post-processed BLIMPS search results with the "blkprob" program to compute
expected values, using combined (for multiple blocks from the same family) 
cutoff evalue = 10. Sorted results by location on each strand.

-----------------------------------------------------------------------------
3. Detailed method:

   Searched 2.9mb DNA sequence vs Blocks+ (15June99, http://blocks.fhcrc.org)
and vs blocks extracted from Smart 3.0 multiple alignments 
(http://coot-embl-heidelberg.de/SMART/) using BLIMPS 3.2.5, which translates
the DNA sequence in all 6 frames for comparison with blocks.
Post-processed BLIMPS search results with the "blkprob" program to compute
expected values, using combined (for multiple blocks from the same family) 
cutoff evalue = 10. Sorted results by location on each strand.

   Removed the following types of results:
	a. Unsupported alignments to single blocks known to be compositionally
	   biased (not supported by other blocks from the family).
	b. Unsupported alignments to single blocks with evalue > 1.
Manually investigated regions where blocks from different families hit
in the same region. 

   The GFF file contains one record for each block, so if 
multiple blocks were hit for a family there will be multiple records.
Documentation for hits can be found at:
	  http://blocks.fhcrc.org/blocks-bin/getblock.sh?<block name>
Searching each strand took about 24 hours and manual post-processing 
about 4 hours by one person.
	  
-------------------------------------------------------------------------
4. References
	  
J.G. Henikoff, S. Henikoff &  S. Pietrokovski, "New features
of the Blocks Database servers", Nucl. Acids Res. 27:226-228 (1999). 

S. Henikoff & J.G. Henikoff,
"A Protein Family Classification Method for Analysis of Large
DNA Sequences." Proceedings of the 27th Ann. Hawaii Intl. Conf. on
System Sciences pp. 265-274 (1994).

S. Henikoff & J.G. Henikoff,
"Protein family classification based on searching a database
of blocks." Genomics 19:97-107 (1994). 

-------------------------------------------------------------------------
5. URLs

http://blocks.fhcrc.org
http://blocks.fhcrc.org/blocks-bin/getblock.sh?<block name>