
                            EMBOSS: newcpgreport
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                             Program newcpgreport
                                       
Function

   Report CpG rich areas
   
Description

   This application is used in the production of the CpG Island database
   'CPGISLE'. It produces CPGISLE database entry format reports for a
   potential CpG island.
   
   See the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the
   finished database.
   
Usage

   Here is a sample session with newcpgreport.

% newcpgreport
Input sequence: embl:rnu68037
Window size [100]:
Shift increment [1]:
Minimum Length [200]:
Minimum observed/expected [0.6]:
Minimum percentage [50.]:
Output file [rnu68037.newcpgreport]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -window             integer    Window size
   -shift              integer    Shift increment
   -minlen             integer    Minimum Length
   -minoe              float      Minimum observed/expected
   -minpc              float      Minimum percentage
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -window Window size Integer 1 or more 100
   -shift Shift increment Integer 1 or more 1
   -minlen Minimum Length Integer 1 or more 200
   -minoe Minimum observed/expected Number from 0.000 to 10.000 0.6
   -minpc Minimum percentage Number from 0.000 to 100.000 50.
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.newcpgreport
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   One or more nucleic acid sequences.
   
Output file format

   Here is the output file from the example run:
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ID   RNU68037  1118 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       157..389
FT                    /size=232
FT                    /Sum C+G=152
FT                    /Percent CG=65.24
FT                    /ObsExp=0.73
FT   CpG island       654..963
FT                    /size=309
FT                    /Sum C+G=206
FT                    /Percent CG=66.45
FT                    /ObsExp=0.96
FT   numislands       2
//
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Data files

   None.
   
Notes

   None.
   
References

    1. Larsen F., Gundersen, G., Lopez L., Prydz H. CpG island as Gene
       Markers in the Human Genome Genomics 13:1095-1107 (1992)
       
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   cpgplot      Plot CpG rich areas
   cpgreport    Reports all CpG rich regions
   geecee       Calculates the fractional GC content of nucleic acid sequences
   newcpgseek   Reports CpG rich regions
   
Author(s)

   This application was written by Rodrigo Lopez (rls@ebi.ac.uk) European
   Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton,
   Cambridge, CB10 1SD, UK.
   
History

   Written (1999) - Rodrigo Lopez.
   
Target users

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