mafft and muscle are both faster than clustalw and on average more
accurate. You can also use different options for mafft to push for speed
or accuracy depending on your needs and patience. Tcoffee has a flavour
that includes structural information if available to assist alignment.
Another flavour, MCoffee, runs a set of different alignment programs,
including clustalw, mafft ..., and assembles the most consistent
alignment based on all of them. If you are dealing with a non-trivial
alignment and its accuracy matters to you then you should always take a
look at it because even the best programs sometimes make obvious
mistakes. It can also pay off to use two alignment programs based on
different methodologies. But don't waste too much time staring at poorly
defined regions as they may simply not be structurally or evolutionary
equivalent.
Bart
On 12-05-15 03:50 AM, martyn.w...@stfc.ac.uk wrote:
Certainly different programs and different scoring matrices will give different
answers. There is not necessarily a correct answer either, just different
educated guesses. With high sequence identity, the answers should be fairly
consistent. As you reduce the sequence identity (i.e. as it gets more
interesting) then the answers will vary more.
I think clustalw is generally considered to be one of the poorer multiple
alignment programs these days (though I am sure opinions will vary here). By
poor, I mean it struggles in the twilight zone of 25 - 30% seq identity, but is
perfectly adequate for routine use. There are many other programs to choose
from: probcons, mafft, TCoffee, Muscle, etc etc. In some tests of MrBUMP, we
found some marginal cases that relied on using an alignment from probcons or
mafft, rather than clustalw.
HTH
Martyn
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: 15 May 2012 08:20
To: ccp4bb
Subject: Re: [ccp4bb] Off topic about program for multiple protein
sequence alignment
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Dear Donghui,
even within one program (clustalw) you would get different results by
picking different weighting schemes (clustalx: Aligment->Alignment
Parameter -> Multiple Alignment Parameter: BLOSUM, PAM, Gonnet...).
As with any software I would assume the developers know best what they
are doing and recommend to stick to the defaults unless you know what
you are doing.
Regards,
Tim
On 05/15/12 08:02, wu donghui wrote:
Dear all,
I want to know your suggestions about current protein sequence
alignment programs. It seems that different programs give different
alignment results such as from analysis of Clustal W and MULTALIN.
Thanks for any input or comments.
Best regards,
Donghui
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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