Generating Codon Usage
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14.1 years ago
Arvalon ▴ 30

Are there any online services or biopython scripts that will calculate the codon usage average for all sequences in a file not individually for each sequence. I only know python, unix and a little bit of perl.

codon • 12k views
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Not sure what is meant by "codon usage average". Perhaps you mean "frequency" ?

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14.1 years ago
Neilfws 49k

The EMBOSS program cusp takes one or more nucleotide sequences as input and outputs codon usage data, looking like this (first few lines):

#CdsCount: 1

#Coding GC 67.79%
#1st letter GC 67.88%
#2nd letter GC 46.89%
#3rd letter GC 88.60%

#Codon AA Fraction Frequency Number
GCA    A     0.077     7.772      3
GCC    A     0.462    46.632     18
GCG    A     0.462    46.632     18
GCT    A     0.000     0.000      0
....

There are a number of EMBOSS servers if you want to run the analysis online.

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3
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14.1 years ago

Not online but CodonW does this.

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Web interface is here.

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CodonW is good for PCA.

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14.1 years ago

For the web services, you can find some services in the BioCatalogue.

You can then run those services with Taverna.

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14.1 years ago

You could try http://www.bioinformatics.org/sms2/codon_usage.html and their codon usage tool. There is a mechanism to use the tool off-line. See link on the above page. I have no experience with this tool, but you may need to concatenate your individual sequences into one.

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11.2 years ago
Naren ▴ 1000

CodonW can concatenate genes to one sequence and then calculates the overall codon usage offline on Windows.

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6.0 years ago
anamaria ▴ 30

Leaving this here for the future reference... Following up on the concatenation approach, you could make use of the Bioconductor packages in R to do this: concatenate the sequences using Biostrings, and then analyse codon usage with coRdon.

https://bioconductor.org/packages/release/bioc/html/Biostrings.html

https://bioconductor.org/packages/release/bioc/html/coRdon.html

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