chips calculates Frank Wright's Nc statistic for the effective number of codons used.

Here is a sample session with chips. If the sequence extends beyond the coding region, the start and/or end positions of the CDS must be provided. chips analyzes only protein coding regions:

% chips -sbeg 135 -send 1292 Input sequence: embl:paamir Output file [paamir.chips]:

Mandatory qualifiers:

[-seqall] (seqall)

Sequence database USA.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-cfile (codon)

Codon usage file.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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