When you need to see the “big picture” in molecular biology then you need to take a look at the whole genome of the organism that are interested in.
From what I’ve seen, most people don’t do this; the general workplan that I’ve seen is that researchers only ever delve into the genome to look for a specific gene/protein sequence (unless of course their work involves genome analysis, phylogeny etc).
That’s a shame because not only does taking the whole genome view help you keep a perspective on the system you are working on, it can also be extremely useful for with strategies such as knock-ins and homologous recombination where having a rough idea of what surrounds your sequence of interest can be invaluable. So maintaining a good understanding of how to use them is a valuable tool.
A number of online and offline genome are viewers available, each with it’s own set of pros and cons. Here is an overview three that I have tried.
Artemis
Artemis is a genome viewer available from Sanger Institute. Its a java based tool with a 3-paned interface window that depicts the genome at various resolutions. Alternating between the different resolutions is a bit tricky but once you get a hold of it shouldn’t be difficult. There is a also search tool that allows your to track down the particular feature that you’re looking for.
A great feature of Artemis is that it allows you to edit the sequence annotations and features. Although the tool isn’t perfect and is a bit finicky at times, it gets the job done.
Artemis supports the most common filetypes -EMBL, GENBANK, FASTA or raw format. Extra sequence features can be added in in EMBL, GENBANK or GFF format.
The best thing I like about Artemis is that there is a web version as well as an offline version, which means once you get used to it you can run it on or offline on any computer anywhere that has java.
Apollo
Apollo genome viewer is another java based genome viewer and annotation tool. It is a part of the Gmod project which runs most of the online genome viewers. The tool came out of a collaboration between the Berkeley Drosophila Genome Project and The Sanger Institute.
Apollo has a similar set of features to Artemis provides, but I found the interface to be less user-friendly. But that’s just a personal opinion so you would be best to have a go at using both Artemis and Apollo and decide for yourself which is best. Again, the user guide will help you make best use of Apollo.
The NCBI Genome Workbench
The NCBI Genome Workbench is far more than just a genome viewer. As the name suggests, it is a complete and customizable workbench of tools that allow you to organize sequence data, which you can retrieve from NCBI databases or from your own files, for a project then view and manipulate them in a variety of ways. There is no online version available but downloading and installing NCBI genome workbench is quite simple.
The software allows you to view sequences as flat sequence files, phylogenetic trees, alignments and more.
The excellent zoomable graphics mode is the real strength of this package. It allows you to easily explore your sequence data at different levels of detail – individual genes can be viewed alone or in their genomic context and can be BLASTed straight from the graphical view. A nice set of alignment analysis tools is also available and BLAST and analysis results can be saved to your project making this a great way to keep track of your sequence data and analyses.
The tool supports quite a number of file formats, and I had no problems working with FASTA and most other file formats however when I tried to import the complete 1st chromosome of Dicyostelium which is in a GFF3 format the program kept crashing repeatedly, so clearly some bugs still need to be ironed out.
The NCBI genome workbench is a great idea, and provides a number of useful tools that make the program a must-have but the interface is a bit clunky and takes some getting used to. However, the site has a comprehensive set of instructions/tutorials to help you get up the learning curve quickly.
What’s your tool of choice?, drop us a line in the comments.
Photo: Semi-detached
The best genome browser is UCSC. It’s google’s first hit when you search for “genome browser” and with a reason. I can try to write a post on it but this will take some time. Try openhelix’s genome browser tutorial (a video) is want to get an impression.
@ Max,
You’re right max, the UCSC genome browser is one of the best genome browsers, but it is not available for offline use, which is what i was interested in.By the way would be great if you could make a post on the UCSC genome browser, would be helpful for users like me.
Great post. I like it. Thank you.
Which is best if you want to compare genomes? A problem is that most of them are based on genome alignments, but if you compare e.g. bacterial genomes, DNA alignments is not that useful unless they are very closely related. You would like to compare the genomes on protein level (like microbesonline.org) instead, based on a tblastx alignment.
I had a hard time with Artemis this semester. It’s a nightmare to browse the genome.
Btw, there’s a typo in third paragraph.
“That’s a shame becuase” << it’s because. :)
I find CLC-Free Workbench useful. It is a little like Vector NTI but has no Problems loading whole Genomes as Genebank files. Good search for Genes, statistics, Alignments….
BTW love this Blog….
@WTJ Thanks for the headsup on the typo! As i said artemis isn’t easy to use, but its better than the other options available ;-)
@Kurt I haven’t tried comparing genomes, but I’m also curious to see how that would go – or may be somebody might come up with a solution in the comments :-)
It seems as if Artemis with the accompanying ACT can use both blastn (DNA) or TBlastX (DNA translated against DNA translated), see more at:
http://www.sanger.ac.uk/Software/ACT/
or test it online:
http://www.webact.org/
@Kurt
Thanks Kurt, funny i never tried the ACT tool that came along with Artemis! Just played around with artemis, which was what i was looking for and missed ACT! You’re right ACT is for genome comparisons, just learnt that from the examples page at http://www.sanger.ac.uk/Software/ACT/Examples/ .I’m glad the post on Artemis could direct you to ACT.
@Kurt: If you want to compare bacterial genomes, I’ve seen a demo once of the mauve aligner, nice interface. You might also have a look on M-GCAT once, it’s a whole-genome alignment visualizer as a standalone app.
@Bala: Why would anyone insist on stand alone software these days? I assume that the days of non-browser based software (except: multimedia applications) are numbered… I prefer online genome browsers, they are more up-to-date and I don’t have to download 50 GB of genomes to start working… (well, i’m working on vertebrates, not bacteria… :-)
@Max: If you have your own proprietary sequenced genome you just don’t upload it anywhere. The article on the Genorama genome viewer contains a table with a comparison of some 19 different genome viewers:
Gans JD, Wolinsky M.
Genomorama: genome visualization and analysis.
BMC Bioinformatics. 2007 Jun 14;8:204.
PMID: 17570856
@Kurt
Thanks for the update, the paper is a must read for anybody looking forward to use genome viewers and tools thereof.
@Max
Apart from what Kurt added when you do have a inhouse database its much easier to access it offline, than be resticted by a cumbersome interface online.Besides, you just need to do that gigabytes of download once, after which there are scripts that will just download the updates! That’s just my opinion ;-)
I like the IGV (Integrative Genomics Viewer) out of the Broad Institute.
Even i like IGV.
Are there any tools equally good like IGV which can be embedded within a web-page?
somehow my comment ended up on the wrong article.