EMBOSS: newcpgreport

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: 

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
//

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 nameDescription
cpgplotPlot CpG rich areas
cpgreportReports all CpG rich regions
geeceeCalculates the fractional GC content of nucleic acid sequences
newcpgseekReports 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