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EMBOSS: newcpgreport |
See the FTP site: ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/ for the finished database.
% 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]:
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) |
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 //
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 |