Question: Package for characterizing amino acid distribution
gravatar for phytobio
2.0 years ago by
San Diego CA, Scripps Institution of Oceanography
phytobio30 wrote:

I am interested in characterizing how an amino acid is distributed along the length of a given protein sequence and if that distribution is significantly different from a random distribution of that amino acid over a sequence of equal length. I would like to determine this for each sequence in a fasta file with 1,000s of sequences.

Ideally I would also like to be able to define where the amino acid is enriched in the sequence (N vs C term for example) as well.

Is anyone familiar with any packages (preferably in R) which do something similar?

The closest I have found is the extractCTDD() function in protr, but unfortunately this only looks at the distribution of pre-set groups of amino acids.

Any help would be much appreciated!

sequence R • 614 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by phytobio30
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