Tag Archives: comparative genomics

Virus-resistant cassava (and some software used to get there)

I’ve been very interested in plant genomics projects and it’s been great to see them yield so many interesting papers lately–most recently on the tomato genome and even more on corn analysis. As much as it’s fun to navel-gaze about the human genome for personal genomics, and it is important to get to medical treatments on human diseases–plant genomics projects can help huge numbers of people with basic nutrition. And these are not just the well-insured Westerners. I wish plant genomics was better funded and not under threat…alas.

So it’s nice to see some outreach on projects of this sort. My CLCBio newsletter linked to a nice story and video of the virus-resistant cassava project (VIRCA). Teams from the US and Africa are working on a plant that’s under major threat right now–but is a major source of food for smallholder farmers. This article at the NYT from a couple of years ago provides some background on that issue, and shows photos of the terrible result of a virus infection: Virus Ravages Cassava Plants in Africa. In the video you’ll note that they stress that this is not a project of corporate agriculture–it’s going to be freely available for farmers.

And they mention that they use the CLCBio software to help with that–rarely does anyone highlight the software in these projects, and that made me smile!

Watch the video for some nice views of what plant genomics projects look like, but be sure to check out the additional project details over at the CLCBio page. And if this doesn’t format right, you can watch the video over there too.

Video Tip of the Week: MizBee Synteny Browser

In my last tip of the week I was really pleased about the opportunity to see the data from a paper set up in a custom GBrowse, but it also reminded me of the limitations of some current strategies for visualization that we are facing. In that case one of the things that I wanted was to be able to visualize both nuclear genes + expression with mitochondrial genes + expression. Right now there’s no way to do that easily in a graphical browser (as far as I know).

Improved visualization strategies that offer increased flexibility about the features being viewed, and that scale up to the current data deluge, are both going to be necessary. So when I spotted this tweet about a group doing visualization I was intrigued:

RT @mcmahanl: RT @chlalanne: Check out Miriah Meyer’s work in #dataviz for #bioinformatics, http://t.co/xo5Ei7K (via @FILWD)

The video tip this week is produced by the Meyer team, and you can click on that image to go to the page where you can see it.

Miriah Meyer’s group has as number of interesting visualization projects underway. Check out the list here: http://www.cs.utah.edu/~miriah/projects/ .  The MizBee tool that explores syntenic relationships graphically is the specific focus of the movie, but you’ll see there’s other tools as well.

Proximity, size, orientation and similarity can be visualized with the MizBee Synteny Browser tools, and the video shows how to interact with the browser and to examine features and regions of interest.

I’m also intrigued by the MulteeSum project. And I was wondering if putting that spatial data from the mitochondrial project (nuclear vs mitochondrial) and various tissues could be done with this. It might get at the features I wanted to compare visually from that very cool work. The example in their papers shows expression in a fly embryo that is very compelling. The Pathline tool may offer another way to do that too.

It’s great to see these efforts to manage and visualize the tremendous volume of data. I think if I was able to do another post-doc at this point that would be a great place to get immersed in something that’s really crucial for the future.

Quick links:

Meyer’s group projects: http://www.cs.utah.edu/~miriah/projects/

MizBee specifically: http://www.cs.utah.edu/~miriah/mizbee/Overview.html

References:

Meyer, M., Munzner, T., & Pfister, H. (2009). MizBee: A Multiscale Synteny Browser IEEE Transactions on Visualization and Computer Graphics, 15 (6), 897-904 DOI: 10.1109/TVCG.2009.167

Meyer, M., Munzner, T., DePace, A., & Pfister, H. (2010). MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data IEEE Transactions on Visualization and Computer Graphics, 16 (6), 908-917 DOI: 10.1109/TVCG.2010.137

Meyer, M., Wong, B., Styczynski, M., Munzner, T., & Pfister, H. (2010). Pathline: A Tool For Comparative Functional Genomics Computer Graphics Forum, 29 (3), 1043-1052 DOI: 10.1111/j.1467-8659.2009.01710.x

Tip of the Week: Plant comparative genomics using Plaza

ResearchBlogging.orgPlaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots, mosses and algae. There are some obvious tools and data from the homepage, but I suggest you take a look at the documentation and tutorials, you’ll find there is a lot more once you start delving into it. In this tip, I’m going to walk though getting phylogeny of a gene family from a specific clade to illustrate that there is a lot here that you might not see at first.

Plaza: http://bioinformatics.psb.ugent.be/plaza/

For grass comparative genomics you might also want to check out Gramene (tutorial, subscription) and for general comparative genomics, VISTA (tutorial, free) is an excellent resource also.

Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K. (2009). PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants THE PLANT CELL ONLINE, 21 (12), 3718-3731 DOI: 10.1105/tpc.109.071506

Tip of the Week: CoGe (comparing genomes) revisited

I did a tip on CoGe’s tool, GeVo about two years ago and we’ve had a guest post about CoGe from Eric Lyons, the lead developer of CoGe just over a year ago. In our ongoing and occasional quest to keep our tips fresh (and move them to SciVee), I’ve decided to revisit CoGe and one of their tools. CoGe has changed a bit since we last visited it (see some of the changes here). There is a new interface, more documentation and many more tutorials, some new tools and interconnections and a lot more genomes.  I’m going to give a brief introduction to SynMap and going to use it to do a genome rearrangement analysis (a subject of a text tutorial at the site).ResearchBlogging.org

The algorithm selected in the example is QUOTA-ALIGN which is the subject of a recent paper, “Screening synteny blocks in pairwise genome comparisions through integer programming” in BMC Bioinformatics. As the paper conclusion states:

The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons.

And as mentioned, and you’ll see in this tip, “QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl webcite, offering easier access to thousands of genomes for non-programmers.
Tang, H., Lyons, E., Pedersen, B., Schnable, J., Paterson, A., & Freeling, M. (2011). Screening synteny blocks in pairwise genome comparisons through integer programming BMC Bioinformatics, 12 (1) DOI: 10.1186/1471-2105-12-102

Tip of the Week: Dot Plots, Synteny at VISTA

VISTA has added a couple of new features to their great comparative genomics resource, dot plots and synteny browser. They are excellent features and additions, but they are not yet easy to find from the homepage. Today’s tip I’m going to show you where they are and take a quick look at what they do. If you want to look at comparative genomics and synteny, you’ll want to check out this feature.  They linked from Vista-Point (which was added early last year), which you can learn more about in the open-access tutorial here. To learn more about what they do and how to use them, check out the VISTA help section linked here.

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • NWChem for High-Performance Computational Chemistry has recently gone Open Source. (HT GenomeWeb) [Jennifer]
  • DIYGenomics relates an iPhone app that compares consumer genomics collections. [Mary]
  • A poster on BridgeDB, a resource for ID conversions. Hat tip to Chris Evelo. [Mary]
  • Sanger has done a very nice site for personal genomics and general background on the human genome, aimed largely at the general public and at teachers. http://www.yourgenome.org/ [Mary]
  • Nice phylogenetic analysis site for building protein phylogenies and structure predictions: PhyloBuilder [Trey]
  • Wired magazine had a fun take on some metagenomics from the Galaxy team. [Mary]
  • Via tweet: RT @dgmacarthur: 50% of UK respondents would take free genetic testing, but only 5% interested at current DTC prices: http://bit.ly/b7tDvx [Mary]
  • I completely missed World Statistics Day. No fireworks. No cake. Nuthin’. Sigh. [Mary]

Tip of the Week: Comparing Microbial Databases


A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I’ve been exploring & thinking since then & am going to give a very brief comparison of those two resources in today’s tip & I’ll expand the comparison to other resources here in the text of this post.

Continue reading

Tip of the Week: Chromhome, for karyotype level comparative genomics

Usually when we think about comparative genomics data, we are thinking about genomes that are pretty well sequenced, and we want to look at that data with variety of tools and algorithms.  But this past week we saw a question about less-well-sequenced genomes, and we thought it was an interesting inquiry.  The question was: is there a web site that displays comparative karyotype data?  So we went looking. And we found Chromhome.

Chromhome has a very straightforward interface.  You choose a target species.  You choose the probe species.  You click paint–and you get a look at the chromosome level homology.  When the data was performed with actual probes and reported in the literature, that data is provided. At the time the paper was published this consisted of more than 100 data sets.

There is also the opportunity to see inferred painting as well.  I’ll let the Chromhome paper authors describe that strategy:

If species A and species B are mapped on species N, then it is possible to deduce some of the chromosomal arrangements of A on B or B on A with respect to the arrangements of N chromosomes. Many of the species in Chromhome have been mapped on human chromosomes using chromosome painting. It is therefore possible to infer homologies between two species each of which have been hybridized with human probes.

So if this type of comparative genomics may be of interest to you, check out Chromhome.

http://www.chromhome.org/

Reference:
Nagarajan, S., Rens, W., Stalker, J., Cox, T., & Ferguson-Smith, M. (2008). Chromhome: A rich internet application for accessing comparative chromosome homology maps BMC Bioinformatics, 9 (1) DOI: 10.1186/1471-2105-9-168