Dear Donghui, Your implied question seems to be "How do I know whether my MSA is good?" Errors in MSAs arise from two factors. First, due to computational limitations, heuristic methods are used for most MSA programs. As a result, one can never be certain that a progressive MSA method actually gives you the optimum alignment since not all of the alignment space has been searched. Having said that, some programs are better than others at finding reasonable alignments (e.g. TCoffee is better than ClustalW). The second factor is the scoring system itself. The choice of substitution matrix that you use depends on how divergent your sequences are. Ideally, one should try several different matrices and see which ones work best. The gap opening and extension penalties are another matter, since they not only vary between protein families, but within the protein sequence itself. The bottom line is that no matter what method you use, you need to look at the alignment and, if possible, overlay the secondary structure for one or more of the homologs to make sure that gaps and insertions occur in sensible places (e.g. loops), signature sequences line up, etc.
With best regards, Eric -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Tim Gruene Sent: Tuesday, May 15, 2012 2:20 AM To: [email protected] 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-----
