How To Bin Metagenomic Assembled Contigs Using Tetranucleotide Frequency

Question

[Shuixia100]

Hi there,

Did anyone know which tool can calculate the tetranucleotide frequency of fasta file and condust the cluster based on the results.

Im trying to bin my assembled contigs into bins in order to develop draft genome basically following the methodology of a science paper: Hess, M., A. Sczyrba, R. Egan, T.-W. Kim, H. Chokhawala, G. Schroth, S. Luo, et al. “Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen.” Science 331, no. 6016 (January 27, 2011): 463–467.

But I found difficulty when doing the tetranucleotide freq calculation. I do found TETRA, but the software could not handle my dataset with 3G data.

Ive no informatics background, it seems quite simple algorithm. Maybe it had been used in some software package. Please let me know if you know any tool could do this? And hopefully told me about the basic how to, otherwise it is too hard for me to touch into the language. THX a lot.

Kylie

Answer 1

[Sean Davis]

You might want to look at the Bioconductor Biostrings package and in particular, the oligonucleotideFrequency method.

[Shuixia100]

Thanks for your quick reply, could you provide some link of documentation or specifically which command I should use for tetranucleotide freq calculation. THX

[Sean Davis]

Edited post to include the appropriate method.

Answer 2

[cts]

Hey we use tetranucleotide frequencies alot in our lab. One of our postdocs wrote a simple script that with calculate frequencies and give you a simple table.

You can find the source code and install instructions here

Answer 3

[doug.rusch]

You can try this web tool which provides a visual means to analyze the data:

http://gos.jcvi.org/openAccess/scatterPlotViewer2.html

You can upload your own data here:

http://gos.jcvi.org/openAccess/uploadScatterplotForm3.html

The best reference for this would be Inskeep et al, 2010 from PLoS One.