cusp

[Ted Chiang]

Hi,

I have question about the Emboss program cusp.  The program creates a
codon usage table based on the "coding" sequence of the input file.  My
question is how does it determine where the 'coding' (or ORF) sequence
given any DNA sequence when one executes the program without specifying
the -sbeg and -send flags.

ie.

$cusp dna_seq  

How does cusp determine where the coding sequence begins?

As opposed to 

$cusp dna_seq -sbegin 135 -send 192

where the coding sequence is specified.  In the latter case, how does if
the specified region is not divisible by 3, does cusp ignore the latter
few nucleotides?


Thanks.

-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================