Question: Generating Codon Usage
3
gravatar for Arvalon
8.1 years ago by
Arvalon30
Arvalon30 wrote:

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 • 6.4k views
ADD COMMENTlink modified 9 days ago by anamaria30 • written 8.1 years ago by Arvalon30

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

ADD REPLYlink written 8.1 years ago by Neilfws48k
6
gravatar for Neilfws
8.1 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 8.1 years ago by Neilfws48k
3
gravatar for Pierre Lindenbaum
8.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

For the web services, you can find some services in the BioCatalogue : http://www.biocatalogue.org/search?q=codon+usage&commit=

You can then run those services with Taverna http://www.taverna.org.uk/

ADD COMMENTlink written 8.1 years ago by Pierre Lindenbaum114k
2
gravatar for Alastair Kerr
8.1 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

Not online but CodonW does this.

ADD COMMENTlink written 8.1 years ago by Alastair Kerr5.2k
1

Web interface is here: http://mobyle.pasteur.fr/cgi-bin/portal.py?form=codonw

ADD REPLYlink written 8.1 years ago by Darked894.2k

CodonW is good for PCA.

ADD REPLYlink written 5.1 years ago by Nari860
1
gravatar for Larry_Parnell
8.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 8.1 years ago by Larry_Parnell16k
0
gravatar for Fred Fleche
8.1 years ago by
Fred Fleche4.2k
Paris, France
Fred Fleche4.2k wrote:

[?]

http://www.bioinformatics.fr/bioinformatics.php?subsection=Codon%20usage

ADD COMMENTlink written 8.1 years ago by Fred Fleche4.2k
0
gravatar for Nari
5.1 years ago by
Nari860
United States
Nari860 wrote:

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

ADD COMMENTlink written 5.1 years ago by Nari860
0
gravatar for anamaria
9 days ago by
anamaria30
anamaria30 wrote:

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

ADD COMMENTlink written 9 days ago by anamaria30
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: 771 users visited in the last hour