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EMBOSS: 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 |
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 .........
Program name | Description |
---|---|
backtranseq | Back translate a protein sequence |
chaos | Create a chaos game representation plot for a sequence |
chips | Codon usage statistics |
codcmp | Codon usage table comparison |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
freak | Residue/base frequency table or plot |
geecee | Calculates the fractional GC content of nucleic acid sequences |
getorf | Finds and extracts open reading frames (ORFs) |
isochore | Plots isochores in large DNA sequences |
newcpgreport | Report CpG rich areas |
newcpgseek | Reports CpG rich regions |
plotorf | Plot potential open reading frames |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
showorf | Pretty output of DNA translations |
showseq | Display a sequence with features, translation etc |
syco | Synonymous codon usage Gribskov statistic plot |
transeq | Translate nucleic acid sequences |
wobble | Wobble base plot |
wordcount | Counts words of a specified size in a DNA sequence |