Help on Lineup program

Rodrigo Lopez rodrigol at biomaster.uio.no
Thu Mar 3 04:12:31 EST 1994

In article <2l2ohd$ani at mserv1.dl.ac.uk>, <LIUNI at PLAUTO.CSATA.IT> writes:
|> Hi,
|> Could anyone tell me what is the procedure so that the LINEUP program in GCG
|> package to have the possibility of to accept a file with more of 30 sequences.
|> Thank in advance
|> Sabino Liuni

Short answer: YES, but you have to be VERY carefull about what
you do. Some impredictable results may occur:

1. make a copy of the lineup.f source in a directory of your own.
2. make a copy of the lineup.inc file in a directory of you own.

cd ~
mkdir newlineup
cd newlineup
% gcg
% gcgsupport
% getsrc source lineup.f
% getsrc include lineup.inc

3. Edit the lineup.inc file to reflect the following changes:

        Parameter NAMELEN = 11
>>>>>   Parameter HighRow = 15, LowRow = -15
        Parameter MaxSeqs = 500
        Parameter MaxBuffs = 10

	Parameter HighRow = 30, LowRow = -30  !depending on your needs

4. fetch the makefile.template and prepare a system specific makefil

% fetch makefile.template
% toirix makefile.template > Makefile
% emacs Makefile    ! editor = your choice!

5. Go to the section that refers to building a FORTRAN application
   and comment out (delete the '#') the lines that read:

#wordsearch: wordsearch.o
#	$(FC) $(FFLAGS) $(FLDFLAGS) -o $@ wordsearch.o $(LIBS)

replace 'wordsearch' with 'lineup' in all three places and save the

6. make the new lineup

% make

7. You should now have a new lineup executable in your current
   directory. To test this one with your MSF file containing more
   than 30 sequences:

% ./lineup -msf mymsffile.msf     ! NB use './' to test the 'local'
				  ! version.

You are done! 

Please remember that I'm assuming you don't have an exagerately big
alignment and that the fragment length of each sequence must be
kept 'small' (i.e. max 300 aa).

I hope this solves your problem.


* RODRIGO LOPEZ SERRANO  rodrigol at biomed.uio.no - rodrigol at biotek.uio.no  * 
* Norwegian EMBnet node  Tel:xx-47-22958756 Fax:xx-47-22694130            *

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