Block searching is available through the web.
Blimps
Blimps is the program that is used both in the calibration phase of
building the BLOCKS database and in the search of a sequence against
the BLOCKS database. In searching, the input to this program is the
sequence to search with and the database to search against plus some
other parameters that control how the search is done. The output is a
list of the top scoring comparisons of the sequence and alignments
with the blocks. The output of this program is not very human readable
and can contain hundreds of scores.
Blimps was written by Bill Alford and is available for
anonymous ftp at URL
ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/.
Blksort
Blksort is a filter for the blimps output. It reads the output and
manipulates it so that it is easier to read. Blksort also does
analysis of the output to report the most likely correct hits of the
hundreds of returned scores in the blimps output. The probability of
a particular comparison being valid is also computed and reported.
Blksort was written by Jorja Henikoff and is available for
anonymous ftp at URL
ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/analysis/. This will soon be
distributed with the blimps release.
Blocks Keyword Search
This tool is only available via the web.
The Blocks Keyword Search is able to retrieve a block from the BLOCKS database when given a word to search with. The search engine is a version of wais (freeWAIS-sf). The CGI script that interfaces to the wais database is kidofwais.pl which has been modified from the original to interface with Getblock.
freeWAIS-sf was derived from freeWAIS by
Ulrich Pfeifer. kidofwais.pl was derived from son-of-wais.pl
by Michael Grady.
Getblock
Getblock is a program that retrieves the given block number from the
BLOCKS database. In addition to the block the PROSITE database
entry that the block was made from is included. This tools use is in
retrieving a block that was matched in a search.
Getblock was written by Jorja Henikoff
and is available through the web.
Block Maker
The block maker tool is a collection of the programs that are used in
the creation of the blocks database. The most notable tools are motif
and gibbs which build blocks from the sequences with two different
techniques. This is to give some confidence to the results because
the method that the blocks are generated can sometimes create
different invalid blocks with questionable data. This is explained in
more detail in the Block Maker help page. The
NAR paper
"Automated assembly of protein blocks for database searching" also
gives more information on this topic.
The core programs used in the block maker were written by Jorja Henikoff and are available for anonymous ftp at URL ftp://ftp.ncbi.nih.gov/repository/blocks/. The specific programs are listed in the above paper.