From bryanlepore at mail.utexas.edu  Sun Oct 15 02:12:23 2006
From: bryanlepore at mail.utexas.edu (Bryan Lepore)
Date: Sun Oct 15 02:12:30 2006
Subject: [Discuss] multalign iterations
Message-ID: <feb1db20610141812r3f23c376scdf8510f1caf8144@mail.gmail.com>

i'm running multalign in hopes of getting a sequence of unknown structure
aligned with a stamp alignment as follows;
$multalign <<EOF
output_file=$scratch/my_output_file.$date.blc
matrix_file=$amps_path/md.mat
gap_penalty=8.0
constant=8
print_vertical=
block_file=for_amps.blc,3
seq_file=for_amps.seq
EOF

.... and i have this in my .blc fil:
* ITERATION 3
but multalign always reports:
 No iteration value defined - assume a value of 1
.. i see this in all the examples too (`grep ITERATION *.*`).  i fiddled
with spaces and such and made it fail.

i THOUGHT i asked about this before, but couldn't find it on google and the
hard drive i was using at the time failed (a long time ago).

am i supposed to run multalign a couple times?

-bryan
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From bryanlepore at mail.utexas.edu  Wed Oct 18 04:15:09 2006
From: bryanlepore at mail.utexas.edu (Bryan Lepore)
Date: Wed Oct 18 04:15:23 2006
Subject: [Discuss] MAXats
Message-ID: <feb1db20610172015pc086103ua9b104f398d02c59@mail.gmail.com>

i'd like to increase MAXats, but i'm uncertain of whether this is doable the
way stamp is written... or c++ for that matter - i see
"int MAXats" in stamp.h, routines.h - or can i adjust MAX_SEQ_LEN in
poststamp.c?

-bryan
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From tom at compbio.dundee.ac.uk  Wed Oct 18 14:17:53 2006
From: tom at compbio.dundee.ac.uk (Tom Walsh)
Date: Wed Oct 18 14:18:04 2006
Subject: [Discuss] MAXats
In-Reply-To: <feb1db20610172015pc086103ua9b104f398d02c59@mail.gmail.com>
References: <feb1db20610172015pc086103ua9b104f398d02c59@mail.gmail.com>
Message-ID: <45362981.5060700@compbio.dundee.ac.uk>

Bryan Lepore wrote:
> i'd like to increase MAXats, but i'm uncertain of whether this is 
> doable the way stamp is written... or c++ for that matter - i see
> "int MAXats" in stamp.h, routines.h - or can i adjust MAX_SEQ_LEN in 
> poststamp.c ?
    Adjusting MAX_SEQ_LEN in poststamp.c will adjust it only in the 
POSTSTAMP program (you'll also need to change MAXslen in  alignfit.h).
    To set it in the STAMP program, just change the MAX_SEQ_LEN 
parameter in stamp.defaults.

    Tom