Alignments & LineUP

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Fri Mar 18 08:03:00 EST 1994


In <199403180105.AA15407 at wugate.wustl.edu> brett at BORCIM.WUSTL.EDU writes:

>      1-  Find a program that can handle the number of sequences I want
>      2-  Modify LINEUP to do the same.

We did the latter. I append a description on how to do it, posted by Rodrigo
Lopez of the Norwegian EMBnet Node about two weeks ago. As you run GCG under
VMS I modified the description accordingly.

By the way: you may wish to modify PileUp in the same manner.

Regards
  Christoph Gartmann


Newsgroups: bionet.software.gcg
Subject: Re: Help on Lineup program
From: rodrigol at biomaster.uio.no (Rodrigo Lopez)
Date: 3 Mar 1994 09:12:31 GMT

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

$ CREATE/DIRECTORY/PROT=(O:RWED) [.newlineup]
$ SET DEFAULT [.newlineup]
$ gcg
$ gcgsupport
$ COPY gensource:lineup.for []
$ COPY geninclude: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
>   
> to
> 
> 	Parameter HighRow = 30, LowRow = -30  !depending on your needs

4. Edit LINEUP.FOR and replace all occurences of
	Include 'GenInclude:LineUp.inc'
   into
	Include 'LineUp.inc'

5. Compile your modified Lineup

   $ FORTRAN/EXTEND_SOURCE lineup.for    ! line 2708 is longer than 72

6. Link the program

   $ sharelink lineup

7. Run the program
   $ newlineup :== $my_disk:[my_directory.newlineup]newlineup
   $ newlineup

> 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).


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