newcpgreport

newcpgreport

newcpgreport 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.

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]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-window (integer)

Window size.

-shift (integer)

Shift increment.

-minlen (integer)

Minimum length.

-minoe (float)

Minimum observed or expected.

-minpc (float)

Minimum percentage.

[-outfile] (outfile)

Output filename.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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