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[Fwd: alignment queries..]



--
- Dr. Azat Badretdinov 
- The Rockefeller Univ, Box 270 
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail: 
- WWW/URL: http://salilab.org/~azat
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Dear Nick!

replying...
> Question 1:
> 
> What is considered to be the minimum length of a sequence motif
> necessary to derive meaningful constraints from the alignment to use in
> modeling.. one, two, three, or more?
> 
> i.e.
> 
> template     -K- -YI- -EEE- -YSIG- -DIDAP-
> target       -x- -xx- -xxx- -xxxx- -xxxxx-
> 
> The Modeller routines tend to pick out longer motifs than Meme,
> Matchbox, PIMA, BLOCKS, etc.  Smallest motif I have had picked out for
> my sequences using these alternative methods is three a.a.'s...
> 
> what would be the effect of only matching two, or even just one residue
> on the modeling?

Usually more than that (dozens if you want just to detect reliable
similarity, and even more if you want a real model). 
It is good to have at least 35-40% sequence identity to build a model.
Sometimes even 30% is Ok. 

> 
> which brings me to my next query..
> 
> Question 2:
> 
> how rigorous must one be with the alignment?
> 
> given an template of, say, IPSDC would it be okay to match VPGCC, etc..
> trying, in general, to keep acidic matched to acidic, basic to basic,
> rings to rings and hydrophobic to hydrophobic, bulky to small, as shown
> in (A)..
> 
> is this the right method - be less worried about the *exact* nature of
> the match, as long as they are physically/chemically similar.. else, is
> it best to mix and match among templates, as illustrated in (B)
> 
> (A) is this acceptable?
> 
> template 1  LPSDC
> template 2  VQSAC
> template 3  IPSEC
> template 4  VPGCC
> target      IPSDC
> 
> (B) or should I break it up like this?
> 
> template 1  L-P-S-D-C
> template 2  V--QS--AC
> template 3  -IP-S--EC
> template 4  V-P--G-CC
> target      -IP-S-D-C
> 
> I believe that this is the critical step in the whole procedure, so
> your comments would be greatly appreciated!

I this case I guess you can trust multiple alignment program which will
probably produce case A.

--
- Dr. Azat Badretdinov 
- The Rockefeller Univ, Box 270 
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail: 
- WWW/URL: http://salilab.org/~azat

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