Question: Cluster Peptide Sequences According Their Amino Acid Properties
3
gravatar for Doo
8.9 years ago by
Doo240
Doo240 wrote:

Do you know a tool where I can cluster peptide fregments (length = 13 AA) according their amino acid properties?

e.g.

PIAAIAPSPQQRK
AAIAPSPQQRKEH
ITNWDDMEKIWHH
EIRSFNMPPFPPP

Thanks

clustering • 3.0k views
ADD COMMENTlink written 8.9 years ago by Doo240

Which properties did you have in mind?

ADD REPLYlink written 8.9 years ago by Neilfws49k

hydrophobic, etc...

ADD REPLYlink written 8.9 years ago by Doo240
1
gravatar for Chris
8.9 years ago by
Chris190
Munich
Chris190 wrote:

You could start with the AAIndex database which is a collection of a variety of different amino acid propensities. You then have to decide which one to take and represent each of your fragment as a propensity vector. As mentioned before, you need some similarity measure between two such vectors. An obvious one would be s(v1,v2)=1-|corr(v1,v2)| , corr being the pearsson correlation coefficient. For clustering, I would start with linkage clustering. R has some nice implementations for this.

ADD COMMENTlink written 8.9 years ago by Chris190
0
gravatar for ALchEmiXt
8.9 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

Have a look at the EMBOSS suite of tools (i.e. embedded in usegalaxy.org). It at least gives you the properties either in signatures or in raw values.....who can be clustered for further analysis...

Or did you mean the individual aa properties and not the peptide on its whole?

ADD COMMENTlink written 8.9 years ago by ALchEmiXt1.9k

I suppose he meant aa for each position

ADD REPLYlink written 8.9 years ago by Student90

thanks. yes, aa for each position

ADD REPLYlink written 8.9 years ago by Doo240

Can you elaborate on why you want to do this? Then I maybe can get a better idea of how to solve it. Just clustering on single aa properties...could probably be done by trasslating each peptide into a virtual "properties peptide" and cluster using a custom distance matrix...but as mentioned...the why would greatly help!

ADD REPLYlink written 8.9 years ago by ALchEmiXt1.9k
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