Artemis - DNA sequence viewer and annotation tool

Category Cross-Omics>Sequence Analysis/Tools

Abstract 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.

Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems.

It can read European Molecular Biology Laboratory (EMBL) and GENBANK database [the National Institute of Health (NIH) genetic sequence database, an annotated collection of all publicly available DNA sequences] entries or sequence in FASTA or raw format.

Extra sequence features can be in EMBL, GENBANK or General Feature Format (GFF) [GFF is a format for describing genes and other features associated with DNA, RNA and Protein sequences] format.

Products features/capabilities include:

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 available, 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 display window.

In addition to this basic display, Artemis can plot the results of calculations on the sequence or on any of the Coding DNA Sequence (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.

Annotation --

Artemis is now the main annotation tool used for analysis of microbial genomes at the Sanger Institute.

Note: The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms.

In addition to the sequence viewing capabilities outlined above, Artemis can display the results of numerous analyses on top of the sequence; CDS predictions, Nucleotide-Nucleotide Basic Local Alignment Search Tool (BLASTN), in-frame Nucleotide 6-frame translation-protein (BLASTX), Transfer RNA (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.

Artemis will also run analyses on sets of CDS features, such as FASTA and Protein-Protein BLAST (BLASTP) searches, and allow the results to be viewed directly from the object selected.

Additional information, such as feature colors, 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.

Artemis can also deal with spliced eukaryotic genomes and when multiple gene predictions are available Artemis can display them side by side. Artemis can also perform Human Sequence Annotation.

On-line demo --

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

Additional product from the same informatics group --

ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. In common with Artemis, ACT is written in Java and runs on UNIX, GNU/Linux, Macintosh and MS Windows systems.

It can read complete EMBL and GENBANK entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

The sequence comparison displayed by ACT is usually the result of running a blastn or a Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx) search.

System Requirements

Artemis and ACT need a recent version of Java (at least version 1.5 or higher).

Manufacturer

Manufacturer Web Site Artemis

Price Free

G6G Abstract Number 20200

G6G Manufacturer Number 102969