* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* A solution to practical using Perl scripts from Brian Stevenson 24 May 2004 *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

Scripts can be found in /usr/molbio/perl/. Typing the script name without
parameters usually displays some help about usage...

Copy over data files to your local working directory on sib-dea:

cp -R /net/ludwig-sun1/export/mirror/sib-isrec-www/DEA/module8/B_Stevenson/Practicals/transcriptome_recon/* .

Convert data files to ace format:

% sim_compacter HTR004283_maps		# reformat experimental data
% sim2ace -n -u HTR004283_maps.compact	# convert to ace format
% sim2ace -u HTR004283_tr		# same with Tromer data
% sequence2ace NT_037497.seq		# genomic sequence too
% tag2ace HTR004283_tags		# tags also

Create database directory structure:

% mkdir HTR004283_db
% mkdir HTR004283_db/database
% mkdir HTR004283_db/rawdata
% cp -R wspec/ HTR004283_db/.

Edit HTR004283_db/wspec/passwd.wrm to get write access on DB:

% emacs HTR004283_db/wspec/passwd.wrm &
or
% vi HTR004283_db/wspec/passwd.wrm

Change "Your Windows login name" to ...


Copy ace files to rawdata directory:

% cp *.ace HTR004283_db/rawdata/.

Tar database directory for transfer to Windows:

% tar cvf HTR004283_db.tar HTR004283_db/

Use ftp at DOS prompt in Windows to transfer HTR004283_db.tar to C:\temp

Launch Acedb in Windows, and point to C:\temp\HTR004283_db

Select Edit from main Acedb window to read .ace files [5 files]

Save data

Enter NM_018845 in yellow search box and click Sequence class...

Any questions, send a mail to Brian.Stevenson at licr.org