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cusp |
The output file can be used as a codon usage table in other applications.
% cusp -sbeg 135 -send 1292 Create a codon usage table Input sequence: embl:paamir Output file [paamir.cusp]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -cfile codon Codon usage table name General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.cusp |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehum.cut |
# CUSP codon usage file # Codon Amino acid Fract /1000 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 .........
The 'Fract' column gives the faction of all amino acids coded for by this codon triplet.
The /1000 column represents the number of codons, given the input sequence(s), there are per 1000 bases. This will be an extrapolation if the sequence is shorter than 1000 bases.
If multiple sequences are input then the statistics are given for all of the sequences together, not individually.
Program name | Description |
---|---|
cai | CAI codon adaptation index |
chips | Codon usage statistics |
codcmp | Codon usage table comparison |
syco | Synonymous codon usage Gribskov statistic plot |