EMBOSS cpgplot

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

EMBOSS cpgplot

cpgplot identifies CpG islands in one or more nucleotide sequences.

Quick Start

To use cpgplot upload your input data in most sequence formats, such as fasta, GenBank, Embl, or Emsembl, gcg formats.

Test Data

Test data for this app can be found here: Community Data -> iplantcollaborative -> example_data ->EMBOSS

Input File

The input can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats. For details, please see http://emboss.sf.net/docs/themes/SequenceFormats.html

  • Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS -> Input ->  L46634.fasta

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Check the 'sequence is nucleotide' box
  • Under graphtype choose cps
  • Leave all other options as default

Output File(s)

Standard EMBOSS output sequence file.

  • cpg_graphout
  • cpgout
  • cpg_outfeat

Tool Source