Gene annotation

How to perform gene annotation?

The Coffee genome hub is powered by the Artemis software. Therefore, efficiency with Artemis is required to contribute the improvement of the coffee genome annotation.

Who can contribute?

Anyone willing to edit gene structure or enrich the functional annotations of genes must have an Artemis account. This access is provided under demand but prior to give access, we will make sure of previous experience with gene annotation. We advise you to have a look to the gene annotation tutorial.

You can request an account here.


Troubleshootings with Artemis

  • Issue: Error - could not create the Java Virtual Machine

This error may occur if your computer does not have enough memory or if the Java Virtual Machine used is 32bit. In that case, right-click on the "Edit with Artemis" link and save the the linked JNLP file instead of opening it with Java web start. Then edit that file with a text editor (Notepad on Windows or TextEdit on Mac) to reduce the value of the tag max-heap-size="1280m" to a lower value like "800m" (if you need a value lower thand the initial-heap-size, also change that value as well), save it and open it with Java (double click on the JNPL file).
Here is an example of JNLP content:

<?xml version="1.0" encoding="UTF-8"?>
    <vendor>Sanger Institute</vendor>
    <homepage href=""/>
    <description kind="short">DNA sequence viewer and annotation tool.
    <j2se version="1.4+ 1.4.2" initial-heap-size="768m" max-heap-size="1280m"/>
    <jar href="sartemis.jar"/>
    <property name="" value="Artemis" />
    <property name="artemis.environment" value="UNIX" />
    <property name="j2ssh" value="" />
    <property name="chado" value="
" />
    <property name="ibatis" value="" />
    <property name="offset" value="0" />
    <property name="apple.laf.useScreenMenuBar" value="true" />
  <application-desc main-class="" >