Artemis 4 - the laboratory for genomics and bioinformatics
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1. Documentation Many users will be able to get started right away after viewing the informative user manual In order to keep up with current issues concerning Artemis users may also want to join the mailing list For those seeking more there is a discussion group To sign up send a message to majordomo sanger ac uk with subscribe artemis users in the body of the message Remember this is free software and comes without any warranty Target Users Artemis is targeted toward academic scientists in the business of sequencing annotating prokaryotic or lower eukaryotic genomes It remains one of the few tools of its kind for the university environment It s free and requires only intermediate computer skills to use and it will work for anything from a junior sized gene to a whole genome http news bmn com hmsbeagle 117 reviews sreview print yes Page 4 of 5 Magazine Beagle Review 9 4 03 4 54 PM Publisher information Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK Tel 44 0 1223 834244 Fax 44 0 1223 494919 Email Artemis developers artemis sanger ac uk Web site www sanger ac uk Software Artemis v4 Pricing structure structure Free Artemis version 4 is available under the terms of the GNU General Public License Software class Data analysis and visualization Molecular ee Matt Carson is the director of bioinformatics Unix systems administrator at the University of Oklahoma Hea2. hands is the zoom functionality Artemis has two main windows a lower DNA protein sequence view and the feature view above Each window implements a zoom function as a side scroll bar allowing the user to zoom into or out of the sequence displayed This might sound like a neat feature but if you use Artemis for a while you will inevitably click in this scroll area and accidentally zoom out to an aerial view or into a base by base view of your genome that you can make no sense of whatsoever I have found many other features that are useful as well although which are thought most useful depends greatly on the particular project One of my favorites is the feature selector This search utility allows the user to look for features by key CDS gene etc qualifier product EC number etc or any text within the feature This is very handy for making a specialized TAB file containing for example only ABC transporters Artemis also includes a great navigator that makes searching through a genome by text key base pattern or amino acid string easy The user can display GC and AG percent and deviation a GC frame plot or correlation scores for the entire sequence There is also a lot of information about each ORF such as a full statistics page containing everything from molecular weight to the percentage of each codon and amino acid and hydrophobicity and hydrophilicity plots On Unix and Linux systems the run menu allows the user to execute a
3. Magazine Beagle Review 9 4 03 4 54 PM To print use Control P PCs Command P Macs or File gt Print SOFTWARE REVIEW Artemis 4 A Artemis Reviewed by Matt Carson Posted December 21 2001 Issue 117 Installation Very good Learning curve Domaro cau Web sunk and word process Good but use of more advanced features may take a little time Technical support air Features Very good Customizability Very good Utility to biologists Very good Overview Within the last several years genome sequencing has become a major focus of both big business and academic science Unfortunately the latter often does not get a chance to take advantage of many of the more powerful tools used in these undertakings due to their large price tags Luckily there is Artemis Artemis is a DNA sequence viewer and annotation tool with a wide variety of resources for biologists Developed at the Sanger Centre in Cambridge UK this program is very useful for analyzing sequence creating informative European Molecular Biology Laboratory EMBL files and preparing projects for submission to GenBank Artemis displays contiguous DNA sequences It translates the DNA into the six possible reading frames and displays the translations in a scrolling window along with the forward and reverse strands of the DNA sequence Sequence features and stop codons are displayed in a synchronized scrolling window above the protein and DNA sequence Each feat
4. configuration of Linux box G3 Macs with 256 to 640Mb memory 400 and 500 MHz processors Solaris 7 and 8 Red Hat Linux 7 1 Windows 2000 and Mac OS 9 Price Free How Long Did It Take to Learn to Use It Productively I began using Artemis a little over a year ago At the time my lab was about to begin the annotation of Neisseria gonorrhoeae and five or six of us were going to be working most of each day for about two months to complete two passes through the genome None of us had ever done this before Setting up this operation required a few days and involved performing a batch BLAST on the genome and parsing the best hits with a Perl script After playing with the software for a day or so we were off and annotating The time it takes to produce results with Artemis depends on what the user wants to do Viewing a DNA sequence is very easy and should take no more than five minutes to master but setting up a large scale annotation project may require some knowledge of shell scripts and Perl as well as a few days to experiment with Artemis Advanced administration may require some knowledge of Unix itself as significant functionality can be tied to Artemis by the appropriate combination of external software and custom scripts Artemis is not something to be afraid of however The format is fairly intuitive and for those who ve spent a little time with computers it should not be difficult to figure out how to make the software work Produc
5. lth Sciences Center s Laboratory for Microbial Genomics s E mail this article to a friend Want to see a review of particular software Send a suggestion a Previous Beagle Software Reviews gt Storyspace 2 for Macintosh Reviewed by Charlie Schick Posted December 7 2001 Issue 116 gt PHP 4 Reviewed by Marijan Adam Posted November 23 2001 Issue 115 gt JFile 5 0 Reviewed by Charlie Schick Posted November 9 2001 Issue 114 gt Dreamweaver 4 Reviewed by Robyn Ness Posted October 26 2001 Issue 113 gt REALbasic Professional Edition 3 5 Reviewed by John Ray Posted October 12 2001 Issue 112 gt ACLUSTER 2 0 Reviewed by Virginia Fitzpatrick Posted September 28 2001 Issue 111 more http news bmn com hmsbeagle 117 reviews sreview print yes Page 5 of 5
6. ny of various types of BLAST searches or a sigcleave analysis on any feature And thankfully Artemis cooperates well with the Concurrent Versions System CVS which is very handy if you re lucky enough to have company when doing your annotation Version 4 provides many improvements over previous versions including bug fixes as well as some new features such as the ability to read the output of MSPcrunch a BLAST post processing filter and new support http news bmn com hmsbeagle 117 reviews sreview print yes Page 3 of 5 Magazine Beagle Review 9 4 03 4 54 PM for running the Clustal W and Jalview multiple alignment editors It should be noted however that the use of these advanced programs may require shell scripting or Perl programming ability See the Artemis release 4 page for details Limitations The Windows and Macintosh versions of this software are not as fully developed as the Unix and GNU Linux versions nor are they as well supported I highly recommend running the Unix or Linux versions for large scale annotation not only because of the stability of the operating system but also because of extra options such as immediate BLAST analysis of ORFs from within the program On the other hand Artemis can run quite slowly at times especially on Unix and Linux systems when viewing very large genomes This problem may be worse if the machine it is running on is equipped with a version of Java greater than 1 1 x From my experience
7. ough it doesn t actually work within Artemis can also be very useful for preparing files for import or export Ability to Import and Export in Different File Formats Artemis takes raw and FASTA files for DNA sequence and GenBank GBK EMBL TAB or GFF GFF files for sequence feature tables When provided with an accession number the Unix and Linux versions allow the user to import entries from the European Bioinformatics Institute EBI Artemis will export DNA or protein sequence in raw FASTA EMBL or GenBank formats Useful or Unusual Features One unique feature of Artemis as a sequence and feature viewer is that it does not require all features to be contained in a single GenBank or EMBL sequence definition file Once you ve loaded a genome or other sequence you can overlay as many different annotations or combinations of annotations on the sequence as you wish simply by loading additional EMBL format files that define the locations and feature identifiers for the additional features you wish to display This turns out to be particularly useful for situations in which you want to have auxiliary information displayed but not included in your main annotation For example the maintenance of a simple EMBL file containing sequence boundaries for spanning a large insert library allows quick indexing into that set whenever a sequence ambiguity shows up in a particular feature Another unusual feature and one not particularly useful in my
8. t Quality Ease of installation Good Precompiled binaries are available for all platforms but you must have Java installed User friendliness Fair to good Interface Good Java GUI Advanced use of Unix GNU Linux versions may require launching from the command line Intuitiveness of Good design Customizability Users can customize a large number of features by altering the artemis etc options file Everything from font size to user defined qualifiers is specified here in plain text which allows the user to tailor the program to his or her specific needs The Windows and Macintosh versions are not quite as easy to customize because the program comes in binary http news bmn com hmsbeagle 117 reviews sreview print yes Page 2 of 5 Magazine Beagle Review 9 4 03 4 54 PM form and you must extract this file with a zip utility before you can alter it Artemis will then read this options file if you place it in the directory where you installed the Artemis binary Ability to Program in Scripts Add Extension Modules etc Source code is freely available from the Sanger Centre FTP site for those with a knack for Java Plot type data created in any external program can be loaded into Artemis and displayed against the DNA sequence view You can add shell scripts to the artemis directory to run custom analyses or perform any desired data manipulations The availability of programming experience is essentially the only limiting factor Perl alth
9. the Macintosh and Windows versions stand out in this area so for speed of display one of these may be the better option Comparisons with Similar Software I honestly can t say I ve spent much time with comparable software Most of the software used to accomplish the same tasks as Artemis are proprietary and being employed at a university I usually use free software if it will do the job The closest comparison I have seen is a free program called AceDB a genome database system used primarily for larger eukaryotic genomes Another somewhat similar program is Sequencher although it is not an annotation tool and is really only similar in that it displays DNA sequence Recently I ve had the opportunity to test DNAMAN as well as the Lasergene package from DNAStar Both of these packages provide considerably more functionality than Artemis such as the ability to switch to alternate genetic codes label restriction enzyme cut sites and perform multiple sequence alignments They also have some disappointing limitations such as the lack of Unix versions and limited interoperability which could hamper their utility in high throughput applications After having tested these commercial applications for a while I would recommend Artemis for the researcher looking for a cross platform and collaborative sequence and annotation viewer and the commercial applications for those who need to do a considerable amount of sequence analysis Technical Support and
10. ure has an edit window where you can add information such as feature number annotator name and product A large list of identifiers for example poly A signal and gene is available The base range is also visible and can be edited manually If a batch BLAST search is performed the entire list of results for each open reading frame ORF can be viewed in its own window http news bmn com hmsbeagle 117 reviews sreview print yes Page of 5 Magazine Beagle Review 9 4 03 4 54 PM I have found myself using Artemis at least every other week to format data for input into other programs such as circular and linear map scripts and local BLAST database creation tools Following the Unix tradition of freely available top notch software Artemis is an application that proves itself useful beyond what you might expect from freeware Available Unix GNU Linux Macintosh Windows platforms System Artemis is designed to function on any machine with a recent version of Java installed For Unix requirements and GNU Linux any version of Java higher than 1 1 1 is sufficient although Artemis was developed using 1 1 7 It is highly recommended that you use the Sun s Java and not the default GNU Linux Kaffe distribution For Windows you need Java version 1 2 or better Macintosh users need Macintosh Runtime for Java MRJ 2 2 or better Test platforms 30 MHz SuperSparc with 64 Mb Main memory 250 MHz UltraSpare with 512Mb just about every possible
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