                                  infobase



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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

Return information on a given nucleotide base
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-code]              string     [ABCDGHKMNRSTUVWXY] Enter IUPAC nucleotide
                                  base codes, e.g. A, C, G, T, R, Y etc. (Any
                                  string)
  [-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 and exit. 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
   -version            boolean    Report version number and exit


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 (c) 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
