Project 3 > Artemis

Artemis DNA sequence viewer

View primers, exons, and mutations as annotations to genomic and protein sequence using the Artemis DNA sequence viewer, a freely-available software application developed by the Sanger Centre that allows a user to navigate through a genomic sequence and its translation.

We have created downloadable Artemis feature tables for the genes included in the CardioGenomics sarcomere gene mutation database. These tables highlight the locations of known mutations in a gene sequence, as well as locating the primers and amplimers we use in our own mutation-detection efforts.

View a screen shot of our Artemis feature tables in use. Mutations, primers, exons, introns, and translations of coding sequence are easily visible along with the genomic sequence. Nucleotide and codon positions are reported for the user's selection.

Downloads

• Download Artemis from the Artemis home page. Artemis is written in Java, and so requires a recent version of Java to be installed on your computer. (It also helps to have a fast computer with lots of memory and a big monitor.) Use the on-line manual for Artemis, or else download the manual as one big file.
• In order for our feature tables to be displayed correctly, please download this version of the file options.txt, and place it in the same folder as the Artemis or "Artemis.jar" application (Macintosh or Windows, repectively), or in the current working directory (Unix).
• Genomic sequence and feature tables for display by Artemis:
  • MYH7: human beta-cardiac myosin heavy chain (sequence | feature table)
  • MYBPC3: human cardiac myosin-binding protein C (sequence | feature table)
  • TNNI3: human cardiac troponin I (sequence | feature table)
  • TNNT2: human cardiac troponin T (sequence | feature table)
  • TPM1: human cardiac alpha-tropomyosin (sequence | feature table)
  • ACTC: human cardiac alpha-actin (sequence | feature table)
  • MYL2: human cardiac regulatory myosin light chain (sequence | feature table)
  • MYL3: human cardiac essential myosin light chain (sequence | feature table)

Usage hints

• Change your monitor's display to 1024 x 768 before you start Artemis.
• Once you have started Artemis, open a sequence file with "File / Open", then select the appropriate feature table with "File / Read an Entry..."
• Pop-up menus are available in each of the three Artemis windows, by pressing the right mouse button on a 2- or 3-button mouse, or by pressing the CTRL or CMD key along with the mouse button on a Macintosh.
• You will probably want to turn off display of stop codons in the top window, using the pop-up menu.
• Note that Artemis is an annotation editor as well as a viewer. You probably do not want to Save your changes before you exit the application!

Notes on some Artemis terminology

• You can think of an "entry" as a file of annotations ("features"), which may or may not have a DNA sequence attached to it. The primary entry will usually be a GenBank, EMBL, or GFF file of genomic sequence Other entries, or "feature tables", are files of features that refer to the genomic sequence in the primary entry.
• A "feature" is an annotation in an entry, consisting of a name, a start position, an end position, and additional information in the form of keys and values. Here's a generalized example of a feature, followed by four actual features from the entry X90780 (a GenBank file).

       --------------------------------
       feature         start..end
                       /key1=value
                       /key2=value
  
       --------------------------------
       exon            4633..4809
                       /gene="TNNI3"
                       /number=7
       exon            6442..6592
                       /gene="TNNI3"
                       /number=8
       3'UTR           6526..6592
                       /gene="TNNI3"
       polyA_signal    6568..6573
                       /gene="TNNI3"
                       /note="putative"
       --------------------------------
        

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2001-09-25