Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. It can read EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

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.

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 each of the plots, you will be able to adjust the window size to suit the zoom level.

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.

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.

The zooming out feature can be used to look at genes in the context of large amounts of flanking sequences.

Requirements:

· Java