alignment software

Mr SMNN Faruque s.faruque at miranda.umds.ac.uk
Sun Mar 19 08:52:24 EST 1995


In article <3kd1pm$s04 at newsbf02.news.aol.com>, djcpoland at aol.com (DJC
poland) wrote:

: Hi,
:      Well, we've got the complete sequence.  It's one of a family of about
: 10 closely related proteins.  I've downloaded ALIGN and made my input file
: of sequences, but when I try to use SCORE, it just sits there with a
: little train engine showing on my powerbook 180 screen and says it's
: forming the initial matrices.  After one hour there is no evidence that
: progress has been made.  Would anyone like to recommend another freeware
: or shareware alignment program that can handle this many 300+ AA sequences
: or assure me that yes it is working, there will be a result when I come in
: tomorrow morning.  I don't mind waiting; I'd just like to be certain that
: something is going on. 

Well we use Macaw (by Greg Schuler) and it is great for DNA and protein
alignments but it can only handle 16 (I think) different sequences at one
time and sometimes it crashes if asked to compare all of them at once.  I
you are alignining 10 sequences of 300+ aa I'd recommend it to you.  If,
however, you're aligning 300+ sequences I'd recommend you try the
following
1) leaving the computer to do it for a LONG time i.e. leaving it overnight
(as I do to my computer when I defragment the disk).
2) inceasing the cut-off score to a very high value and if that works but
doesn't find and alignments lower the score until it does.  
3) failing that doing it by telnet'ing to a big computer and letting it do
all the hard work.

It varies a lot due to programming, but if your computer is low on memory
and you use virtual memory, the computer can lock-up and simply shuffle
data from the disk to memory and back again endlessly.

Hope you have success

Nadeem

NB if you want to use Macaw it can be found in several places inc
ftp.bio.indiana.edu:/molbio/ncbi/macaw.sea.hqx
and the current version (I think) is 2.0.4



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