| geecee

## Function

Calculates fractional GC content of nucleic acid sequences

## Description

This calculates the fraction of G+C bases of the input nucleic acid sequence(s).

It reads in nucleic acid sequences, sums the number of 'G' and 'C' bases and writes out the result as the fraction (in the interval 0.0 to 1.0) of the length of the whole sequence.

## Usage

Here is a sample session with geecee

    % geecee tembl:hhtetra
    Calculates fractional GC content of nucleic acid sequences
    Output file [hhtetra.geecee]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outfile]           outfile    Output file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1             integer    Start of each sequence to be used
       -send1               integer    End of each sequence to be used
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name

       "-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 deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.geecee
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

geecee reads any nucleic acid sequence USAs.

### Input files for usage example

'tembl:hhtetra' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:hhtetra

    ID   HHTETRA    standard; DNA; VRL; 1272 BP.
    XX
    AC   L46634; L46689;
    XX
    SV   L46634.1
    XX
    DT   06-NOV-1995 (Rel. 45, Created)
    DT   04-MAR-2000 (Rel. 63, Last updated, Version 3)
    XX
    DE   Human herpesvirus 7 (clone ED132'1.2) telomeric repeat region.
    XX
    KW   telomeric repeat.
    XX
    OS   Human herpesvirus 7
    OC   Viruses; dsDNA viruses, no RNA stage; Herpesviridae; Betaherpesvirinae.
    XX
    RN   [1]
    RP   1-1272
    RX   MEDLINE; 96079055.
    RA   Secchiero P., Nicholas J., Deng H., Xiaopeng T., van Loon N., Ruvolo V.R.,
    RA   Berneman Z.N., Reitz M.S. Jr., Dewhurst S.;
    RT   "Identification of human telomeric repeat motifs at the genome termini of
    RT   human herpesvirus 7: structural analysis and heterogeneity";
    RL   J. Virol. 69(12):8041-8045(1995).
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..1272
    FT                   /db_xref="taxon:10372"
    FT                   /organism="Human herpesvirus 7"
    FT                   /strain="JI"
    FT                   /clone="ED132'1.2"
    FT   repeat_region   207..928
    FT                   /note="long and complex repeat region composed of various
    FT                   direct repeats, including TAACCC (TRS), degenerate copies
    FT                   of TRS motifs and a 14-bp repeat, TAGGGCTGCGGCCC"
    FT   misc_signal     938..998
    FT                   /note="pac2 motif"
    FT   misc_feature    1009
    FT                   /note="right genome terminus (...ACA)"
    XX
    SQ   Sequence 1272 BP; 346 A; 455 C; 222 G; 249 T; 0 other;
         aagcttaaac tgaggtcaca cacgacttta attacggcaa cgcaacagct gtaagctgca        60
         ggaaagatac gatcgtaagc aaatgtagtc ctacaatcaa gcgaggttgt agacgttacc       120
         tacaatgaac tacacctcta agcataacct gtcgggcaca gtgagacacg cagccgtaaa       180
         ttcaaaactc aacccaaacc gaagtctaag tctcacccta atcgtaacag taaccctaca       240
         actctaatcc tagtccgtaa ccgtaacccc aatcctagcc cttagcccta accctagccc       300
         taaccctagc tctaacctta gctctaactc tgaccctagg cctaacccta agcctaaccc       360
         taaccgtagc tctaagttta accctaaccc taaccctaac catgaccctg accctaaccc       420
         tagggctgcg gccctaaccc tagccctaac cctaacccta atcctaatcc tagccctaac       480
         cctagggctg cggccctaac cctagcccta accctaaccc taaccctagg gctgcggccc       540
         taaccctaac cctagggctg cggcccgaac cctaacccta accctaaccc taaccctagg       600
         gctgcggccc taaccctaac cctagggctg cggccctaac cctaacccta gggctgcggc       660
         ccgaacccta accctaaccc taaccctagg gctgcggccc taaccctaac cctagggctg       720
         cggccctaac cctaacccta actctagggc tgcggcccta accctaaccc taaccctaac       780
         cctagggctg cggcccgaac cctagcccta accctaaccc tgaccctgac cctaacccta       840
         accctaaccc taaccctaac cctaacccta accctaaccc taaccctaac cctaacccta       900
         accctaaccc taaccctaac cctaaccccg cccccactgg cagccaatgt cttgtaatgc       960
         cttcaaggca ctttttctgc gagccgcgcg cagcactcag tgaaaaacaa gtttgtgcac      1020
         gagaaagacg ctgccaaacc gcagctgcag catgaaggct gagtgcacaa ttttggcttt      1080
         agtcccataa aggcgcggct tcccgtagag tagaaaaccg cagcgcggcg cacagagcga      1140
         aggcagcggc tttcagactg tttgccaagc gcagtctgca tcttaccaat gatgatcgca      1200
         agcaagaaaa atgttctttc ttagcatatg cgtggttaat cctgttgtgg tcatcactaa      1260
         gttttcaagc tt                                                          1272
    //

## Output file format

### Output files for usage example

### File: hhtetra.geecee

    #Sequence   GC content
    HHTETRA       0.53

The first non-blank line is the title line. Subsequent lines consist of two columns of data.

- The first column is the name of the sequence.
- The second column is the percentage G+C content of the sequence.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 on successful completion.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cpgplot | Plot CpG rich areas
cpgreport | Reports all CpG rich regions
newcpgreport | Report CpG rich areas
newcpgseek | Reports CpG rich regions

## Author(s)

Richard Bruskiewich (r.bruskiewich@cgiar.org)
while he was at:
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 18th June 1999.

## Target users

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

## Comments

None /BODY>