## BioMotif in ACeDB

Help pager written by Martin Aslett, August '97

BioMotif is an external program, written by Gerard Mennnessier, which can be called from within xace. Its aim is to help the user find Motifs within sets of sequences.

BioMotif is fully documented at http://www.lpm.univ-montp2.fr/~menes/bioMotif_doc/bioMotif_ref.html.

In order to run bioMotif within ACeDB, the sodtware must be fully installed on your machine (it does not come packaged with the standard ACeDB release). The software may be downloaded from :-

ftp://ftp.lpm.univ-montp2.fr/pub/BioMotif/v15b/

This directory contains a README file giving full instructions on how to install the BioMotif software on your machine. Before running BioMotif from within xace, the environment variable BIOMOTIF_DIR should be set to the directory above bioMotif_bin (which contains the BioMotif executable) i.e. the executable file will be found at:-

BIOMOTIF_DIR/bioMotif_bin/bioMotif

BioMotif may be run in xace from the FMAP display, under the 'Analysis' button, either by activating it via the pulldown menu accessible from the button or by clicking the 'Analysis' button and choosing BioMotif from the list of External Analysis Programs. The DNA Analysis window may also be opened directly from the pull down menu of main class window of ACeDB

Once BioMotif is run, the following parameters window is called up :-

A query should be typed into the yellow box. Consult the documentation for details of the query syntax.

One of the three target buttons should be clicked before BioMotif can be run :-

Active Zone - uses the active zone on the current sequence display as the target for your BioMotif query. Active Keyset - uses any sequences in the current keyset as the target. Whole database - uses all of the sequences in the database as the target.

Clicking one of these will cause a 'Search' button to appear in the bottom left hand corner of the window. Clicking this button runs BioMotif. If BIOMOTIF_DIR is set wrongly or the BioMotif software is not installed, an error window will appear informing you that ACeDB couldn't find the software.

If the software runs successfully, BioMotif will report it's results in the parameters window, giving details of the sequences conforming to your search parameters together with details of the base pairs in the sequence which match the search. It will also open a new window titled 'Motifs' containing the same details and a keyset window containing all of the sequences on which the search was successful.

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last edited: Septembre 1997