Cluster Peptide Sequences According Their Amino Acid Properties

Question

[Doo]

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

[Neilfws]

Which properties did you have in mind?

[Doo]

hydrophobic, etc...

Answer 1

[Chris]

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.

Answer 2

[ALchEmiXt]

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?

[Student]

I suppose he meant aa for each position

[Doo]

thanks. yes, aa for each position

[ALchEmiXt]

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!