|   | cutgextract | 
The EMBOSS distribution comes loaded with a set of codon usage tables. Thes codon usage tables provided with the distribution are calculated from the files in ftp://ftp.ebi.ac.uk/pub/databases/codonusage/README), with a few additions whose exact derivation cannot easily be determined. Many people would prefer to create their own from the public CUTG data.
You run cutgextract on the CUTG database from ftp://ftp.ebi.ac.uk/pub/databases/cutg. You should get all the required *.codon files from CUTG, and uncompress them if they are compressed before running cutgextract on them.
The task of downloading the CUTG database and running cutgextract to create the codon usage table files from it would normally be done only once when the EMBOSS package is being installled or if a new version of the CUTG database is released.
Note by the way that CUTG has a drawback: it has a table for each organism without making the distinction between different gene populations.
It then parses out the codon usage data from these *.codon files and writes one file per species into the EMBOSS data/CODONS directory. The names of the files are derived from the species names in the CUTG files. These files names will be long (and therefore descriptive).
| % cutgextract Extract data from CUTG Codon usage directories [.]: data General log output file [outfile.cutgextract]: | 
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-directory]         dirlist    [.] Codon usage directories
  [-outfile]           outfile    [*.cutgextract] General log output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -release            string     CUTG release (Any string is accepted)
   -wildspec           string     [*.codon] Type of codon file (Any string is
                                  accepted)
   -species            string     [*] Species wildcard (Any string is
                                  accepted)
   -allrecords         boolean    [N] Include all records, including those
                                  with warnings
   -filename           string     Single output filename to override automatic
                                  one file for each species. Leave blank to
                                  generate the filenames. Specify a filename
                                  to combine several species into one file.
                                  (Any string is accepted)
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-directory] (Parameter 1) | Codon usage directories | Directory with files | . | 
| [-outfile] (Parameter 2) | General log output file | Output file | <*>.cutgextract | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -release | CUTG release | Any string is accepted | An empty string is accepted | 
| -wildspec | Type of codon file | Any string is accepted | *.codon | 
| -species | Species wildcard | Any string is accepted | * | 
| -allrecords | Include all records, including those with warnings | Boolean value Yes/No | No | 
| -filename | Single output filename to override automatic one file for each species. Leave blank to generate the filenames. Specify a filename to combine several species into one file. | Any string is accepted | An empty string is accepted | 
This directory contains output files.
| Writing EDictyostelium_discoideum.cut CDS: 7 Writing EAphrodite_aculeata.cut CDS: 1 Writing EAedes_aegypti.cut CDS: 23 Writing EAnadara_trapezia.cut CDS: 2 Writing EAedes_albopictus.cut CDS: 2 Writing EAcanthocheilonema_viteae.cut CDS: 2 Writing EAmblyomma_americanum.cut CDS: 2 Writing EAstacus_astacus.cut CDS: 3 Writing EAedes_atropalpus.cut CDS: 1 | 
| Program name | Description | 
|---|---|
| aaindexextract | Extract data from AAINDEX | 
| printsextract | Extract data from PRINTS | 
| prosextract | Build the PROSITE motif database for use by patmatmotifs | 
| rebaseextract | Extract data from REBASE | 
| tfextract | Extract data from TRANSFAC |