New e-mail server for homology searching

Steven Henikoff henikoff at milton.u.washington.edu
Tue Aug 18 13:12:28 EST 1992


        ___________               ___________               ___________ 
       |\ __________\            |___________|            /__________ /|
       | |           |           |           |           |           | |
       | | **********|           |***********|           |********** | |
       | | * BLOCKS  |           |   E-MAIL  |           |SEARCHER * | |
       | | **********|           |***********|           |********** | |
        \|___________|___________|___________|___________|___________|/
                     |\ __________\         /__________ /|
                     | | JC Wallace|       | Copyright | |
                     | |   S Agus  |       |    Fred   | |
                     | |JG Henikoff|       | Hutchinson| |
                     | | S Henikoff|       |   Center  | |
                      \|___________|       |____1992___|/

As an aid to detection and verification of protein sequence homology, we
introduce the BLOCKS e-mail searcher, which compares a protein or DNA sequence
to the current database of protein blocks. Blocks are short multiply aligned
ungapped segments corresponding to the most highly conserved regions of
proteins. A database of blocks has been constructed by successive application
of the automated PROTOMAT system to individual entries in the PROSITE catalog
of protein groups keyed to the SWISS-PROT protein sequence databank. The
rationale behind searching a database of blocks is that information from
multiply aligned sequences is present in a concentrated form, reducing
background and increasing sensitivity to distant relationships. If a particular
block scores highly, it is possible that the sequence is related to the group
of sequences the block represents. Typically, a group of proteins has more than
one region in common and their relationship is represented as a series of
blocks separated by unaligned regions. If a second block for a group also
scores highly in the search, the evidence that the sequence is related to the
group is strengthened, and is further strengthened if a third block also scores
it highly, and so on.

For a detailed help file, send a blank e-mail message as follows:

To: blocks at howard.fhcrc.org
Subject: help

Or just send a protein or DNA sequence in FASTA, Genepro, GenBank, EMBL, SWISS-
PROT, or PIR formats (DNA is automatically translated in all 6 reading frames 
for searching).  Here is an example of a protein query in FASTA format:

To: blocks at howard.fhcrc.org
Subject:
>YCZ2_YEAST   Hypothetical 40.1 KD protein in HMR 3' region
MKAVVIEDGKAVVKEGVPIPELEEGFVLIKTLAVAGNPTDWAHIDYKVGPQGSILGCDAA
GQIVKLGPAVDPKDFSIGDYIYGFIHGSSVRFPSNGAFAEYSAISTVVAYKSPNELKFLG
EDVLPAGPVRSLEGAATIPVSLTTAGLVLTYNLGLNLKWEPSTPQRNGPILLWGGATAVG
QSLIQLANKLNGFTKIIVVASRKHEKLLKEYGADQLFDYHDIDVVEQIKHKYNNISYLVD
CVANQNTLQQVYKCAADKQDATVVELTNLTEENVKKENRRQNVTIDRTRLYSIGGHEVPF
GGITFPADPEARRAATEFVKFINPKISDGQIHHIPARVYKNGLYDVPRILEDIKIGKNSG
EKLVAVLN




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