frequently asked questions on
       color
name
organism
sequence
output format
codon usage tables
codon usage frequency vs. relative adaptiveness new in gcua 2.0

threshold & color
          
threshold
    threshold1 ≥ threshold2
    100 ≥ threshold1 and threshold2 ≥ 0.001
    threshold1 and threshold2 < 100
    Color for threshold 2 overrides color for threshold 1 when threshold1 = threshold2

color
The seven available colors should meet everybody's requirements.
  black yellow red magenta grey green blue

codon usage tables - cut
          
browsing to kazusa
First of all you should open a second browser window, besides that of the GCUA and browse to http://www.kazusa.or.jp/codon/ (or simply hit this link). You will find a heading: "Alphabetical lists of all organisms". Navigate (using the links) till you find the desired organism. Let's assume you are looking for Equine herpesvirus 1. After some clicking you will end up on this page. On this page you'll find a heading "Fomat" below the table. Choose "1:Standard" from the drop down box, do not change the option "Codon Usage Table with Amino Acids", and "Submit". You will get this page.

The url of the page should look like this (one line):
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=48410&aa=1&style=N

Copy the whole url starting with "http://..." and ending with "...style=N" and paste it into the textbox at GCUA. Choose "http_url" from the drop down menu at GCUA.

submiting your own cut:
You can submit your own table if it is accessible via http. If you need helf let me know.

Kazusa output error:
The option to reformat codon usage tables to "A style like CodonFrequency output in GCG Wisconsin Package" is not working properly since Kazusa updated their database in late 2007. The last colum "Fraction" is always "0.00" (example).


output format
          
html
Formating graphical output using html is not possible, but I'll do my very best. This online tools usally should work with the most recent browser versions of Netscape/ Mozilla, MS IExplorer and Opera. Be shure that execution of Cascading Style Sheets is switched on.

pdf
There are known problems with the Adobe Acrobat reader plug-in when using MS IExplorer. If you get a blank page after submission of your job, your version of MS IExplorer features this bug, so switch to another version or to another browser.

email-plaintext
You will get a plain text file via email containing all the information you need to draw your graphs e.g. using Microsoft Excel.

printing
The pdf file is set up to fit to A4 paper size (210mm x 297mm). I am aware of printing problems when using non Post Script capable printers. To my knowledge this problems are caused by bugs in the printer driver software.

Your suggestions
Feel free to mail me.

name
          
A sequence identifier (usually the name of the gene) submitted.

organism
          
If the organism from which your submitted sequence is derived from, is not listed you have to choose "not listed" from the drop down menu and enter a name for the organism. If you type in a name and do not choose "not listed", the value choosen from the drop down menu will be printed into the output file.


sequence
          
sequence textbox
The DNA sequence pasted into the textbox may contain arbitrary white spaces, line breaks, numbers BUT no letters other than A T G C (if FASTA format this is not true for the first line, i.e. the FASTA Identifier).
The DNA has to be in-frame, the sequence length has to be a multiple of 3 and for server load reasons the length has to be <‎10.000 bp.

fasta format
A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The first line, i.e. the FASTA Identifier, overrides the name given in the textbox sequencename.



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