On-line demo

An on-line demo of the software is available to guide the user through some of the basic functionality.

Sequence viewing

Artemis will read features and sequence from disk and display the features on a six-frame translation of the sequence. Two views of the sequence are shown, both of which can be zoomed in to the base level, or zoomed out to display the entire sequence. There is also a list of features at the bottom of the window. This gif shows an example of a cosmid from Bordetella bronchiseptica, EMBL: AJ007747 (click on the thumbnail image to see the full size gif)

In addition to this basic display, Artemis can plot the results of calculations on the sequence, or on any of the CDS features. The sequence plots are tied to the sequence display and scale with it as the zoom level is changed. For all of the plots the window size can be altered dynamically to suit the zoom level. This gif shows the same sequence with a simple %G+C plot for the DNA sequence, and a plot of amino-acid properties for one of the CDS features.

Annotation

Artemis is now the main annotation tool used for analysis of microbial genomes at the Sanger Institute. In addition to the sequence viewing capabilities outlined above, Artemis can display the results of numerous analysis on top of the sequence; CDS predictions, BLASTN, in-frame BLASTX, tRNA and motif searches etc. can all be viewed and incorporated into the annotation. These are all run externally and the results parsed into EMBL-format, meaning that the results of any analysis can be easily incorporated without modification of the Artemis program itself. This gif shows BLASTX, BLASTN and FramePlot results for a Streptomyces coelicolor cosmid SC6A9.

Artemis will also run analyses on sets of CDS features, such as FASTA and BLASTP searches, and allow the results to be viewed directly from the object selected. Additional information, such as feature colours, functional classifications etc. can also be added to the annotation, and the final file written with all this intact, for internal use, or with non-EMBL features removed, for submission to the database. This gif shows the final annotation for the cosmid used above.

The zooming out feature can be used to look at genes in the context of large amounts of flanking sequence; this gif shows a %G+C plot for 200kb of the Mycobacterium tuberculosis genome, showing the extreme GC-richness of the PE-PGRS gene family.

Artemis can also deal with spliced eukarotic genomes, and is used extensively by the Schizosaccharomyces pombe annotation team. This gif shows the highly spliced trt1 gene in the cosmid SPBC29A3.

When multiple gene predictions are available Artemis can display them side by side as in this example from Plasmodium falciparum. The picture shows the results of a tblastx against a related species and gene predictions by Phat and glimmer.

Human Sequence Annotation

Two examples of human sequence annotated in Artemis. The example on the left is from the CHED1 region of chromosome 20 and the example on the right is from the CHED2 region of chromosome 20. The examples show cDNA from human and mouse, mouse genomic dna and exofish gene predictions in parallel.