Pairwise local alignment

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claire84
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Pairwise local alignment

Post by claire84 » Mon Oct 10, 2011 4:32 pm

Hi,
I'm not a bioinformatic, but I need to perform a sequence alignment between two protein which are not very similar. In this case is better to perform a local alignment, right?
I did this kind of aligment with LALIGN tool.What do you think about this tool?

THANK YOU IN ADVANCE!

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JackBean
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Post by JackBean » Mon Oct 10, 2011 6:03 pm

local alignment is best for proteins, which may have the same domain (but others differ), or differ in length in general, or when you look for example for similar residues in the active site.
The homology of sequences should be reflected by homology matrix used (compaire e.g. BLOSUM80 vs. BLOSUM62 or PAM250 vs. PAM100).
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

claire84
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Re: Pairwise local alignment

Post by claire84 » Tue Oct 11, 2011 2:47 pm

Yes, I'm looking for similar residues in the active site of tese two proteins. So, I have to perform cycles of local alignment using different substitution matrix. Is it right? Can I use LALIGN?

thank you!

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JackBean
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Post by JackBean » Tue Oct 11, 2011 3:01 pm

there's no need to use several matrices, just pick one.
I don't have experience with LALIGN, but I guess it should be fine.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

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