
                                 infobase 



Function

   Return information on a given nucleotide base

Description

   infobase reports the defined properties for all known bases, or for
   any bases specified by the user.

Usage

   Here is a sample session with 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

Command line arguments

   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

Input file format

   infobase uses a string of base codes.

Output file format

   infobase outputs a text table of base properties.

  Output files for usage example

  File: outfile.infobase

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

Data files

   infobase reads the Ebases.iub file to define IUB standard codes for
   nucleotides and ambiguity codes.

   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:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   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

Author(s)

   Jon Ison (jison © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
