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 > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPsgOYUxlJ7aRr7hoRArwKAKCqhK2012Ihnof7xjRzyao7GI8xpgCfZj/G > VfD3ly3bmqycO0mX888oYfE= > =7v6r > -----END PGP SIGNATURE-----
