Question: How To Bin Metagenomic Assembled Contigs Using Tetranucleotide Frequency
2
gravatar for Shuixia100
6.9 years ago by
Shuixia100120
HK
Shuixia100120 wrote:

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

ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 6.9 years ago by Shuixia100120
2
gravatar for Sean Davis
6.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Sean Davis25k

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

ADD REPLYlink written 6.9 years ago by Shuixia100120

Edited post to include the appropriate method.

ADD REPLYlink written 6.9 years ago by Sean Davis25k
2
gravatar for cts
6.2 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

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

ADD COMMENTlink written 6.2 years ago by cts1.6k
0
gravatar for doug.rusch
6.9 years ago by
doug.rusch0
doug.rusch0 wrote:

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.

ADD COMMENTlink written 6.9 years ago by doug.rusch0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1456 users visited in the last hour