infobase |
% infobase Return information on a given nucleotide base Nucleotide base code [ABCDGHKMNRSTUVWXY]: Output file [outfile.infobase]: |
Go to the output files for this example
Standard (Mandatory) qualifiers: [-code] string [ABCDGHKMNRSTUVWXY] Enter IUPAC nucleotide base codes, e.g. A, C, G, T, R, Y etc. (Any string is accepted) [-outfile] outfile [*.infobase] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to 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 | |
---|---|---|---|
[-code] (Parameter 1) |
Enter IUPAC nucleotide base codes, e.g. A, C, G, T, R, Y etc. | Any string is accepted | ABCDGHKMNRSTUVWXY |
[-outfile] (Parameter 2) |
Output file name | Output file | <*>.infobase |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
Code Ambiguity Complement Mnemonic A A T adenine B CGT V not_adenine C C G cytosine D AGT H not_cytosine G G C guanine H ACT D not_guanine K GT M keto_base M AC K amino_base N ACGT N any_base R AG Y purine_base S CG S strong_bond T T A thymine U T A uracil V ACG B not_thymine/uracil W AT W weak_bond X ACGT X unknown Y CT R pyrimidine |
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Program name | Description |
---|---|
infoalign | Display basic information about a multiple sequence alignment |
inforesidue | Return information on a given amino acid residue |
infoseq | Display basic information about sequences |
seealso | Finds programs with similar function to a specified program |
showdb | Displays information on configured databases |
textsearch | Search the textual description of sequence(s) |
tfm | Displays full documentation for an application |
whichdb | Search all sequence databases for an entry and retrieve it |
wossname | Finds programs by keywords in their short description |