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    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   

    Wellcome Trust Genome Campus
    Pathogen Informatics Group
    Hinxton, Cambridge,
    CB10 1SA, UK
    Tel:+44 (0)1223 834244
    E-mail: artemis@sanger.ac.uk
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