# Blocks Tools

There are various tools that are used in the Blocks program suite. Here is a list of some of them and a description of each.

### Index:

- Block Search
- Blimps
- Blksort
- Blocks Keyword Search
- Getblock
- Block Maker

### Block Search

A block search uses blimps to do the searching and scoring and blksort to do the interpretation of the data. See the Block Search help page for more details.

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.

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Contact us Page last modified on Oct 1998