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.

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

Plaza, 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

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

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.

• I couldn’t figure out the folklore part, but this handy little interface called Matrix2png takes lists and make a matrix diagram, looked a bit useful to me:   RT @pleonard: Wonder if authors of visualization software for protein sequencing knew it would one day be used on Danish folklore? http://bit.ly/e9HS5v [Mary]
• UGene: http://ugene.unipro.ru/index.html They have recently released a new version, and it looks very nice.. the successor to taverna? [Giovanni, from last week's SNPpets comments]
• New software for comparative genomics: PHAST and RPHAST. [Trey]
• Loved this imagery:  RT @HHMINEWS: Evan Eichler: The evolving human genome as an action-adventure movie with multiple car crashes: http://ow.ly/3Oocv hat tip to @WudIzThePoint [Mary]
• iPlant announcement–very cool. Also note they are looking for software engineers for their projects: RT @plantdisease: InTheNews: A powerful new partnership in plant science http://bit.ly/gJ3PTh [Mary]
• Moving towards integrating genomics into healthcare: RT @eurogene: Combining adv informatics, genomics, consultation, eMERGE 1st step  to inc genomic into routine healthcare http://bit.ly/gYtNHl Hat tip Keith Grimaldi [Mary]
• From BIO SmartBrief, an article on using genomics of tuberculosis pathogens to determine courses of antibiotics for individual patients in the hopes of increasing effectiveness of treatments & decreasing occurrence of microbial drug resistance. How cool is that? [Jennifer]
• CSI genomics: RT @EricTopol: First “molecular autopsy” using whole genome sequencing to establish cause of death http://bit.ly/ffzPBN [Mary]

• Public health in the genomic era, a report by PHG Foundation, is out. You can access it at their site here.  [Mary]
• The 23andme sale continues through Christmas–saliva as a stocking-stuffer? [Mary] (well, we’ve given a few this Christmas ) [Trey]
• Favorite tweet this week is from @genetics_blog: Abstract Art with PubMed2Wordle http://goo.gl/fb/RNOEh
• Much tweet-buzz about this comparative genomics game: Phylo. [Mary]
• Giggle [Mary]: 
• Week of the wiki? Mary mentioned the WikiGene Opportunity earlier this week, I’ve gotten a couple of wiki related email announcements, and the issue of Nature that I go this week has an article entitled “No rest for the bio-wikis” [Jennifer]
• I missed the New York Ensemble Studio Theatre run of Photograph 51, a play about Rosalind Franklin, her science and her struggles (described in this Nature article, requires subscription or payment). Hopefully the play is picked up by other theaters, including one near me. [Jennifer]
• Mary & I both received announcements of the release of Version 2.0 of The GeneMANIA Cytoscape Plugin for Gene Function Prediction. You can read about it here. [Jennifer]
• The 10,000 Genome Project (G10K) announces the selection of it’s first 101 species. Go to the G10K site, click  on the Accomplishments box on the right to see the list. I’m quite certain it’s the first time I’ve ever seen the species “Wuchang bream”. And what’s a Coqui? I know Koalas. Cool.  [Mary]
• Something to consider: “Are Women the Key to Sustainable Development?” [Jennifer]

• 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]

Each of these resources could (and does in many cases) have an hour long tutorial devoted to it so I will only be able to give the briefest of overviews in this 5 minute tip, but I think (hope) it will be enough to get you thinking and exploring. The way I see things, comparing these two resources is kind of like comparing apples and aardvarks: they start with the same thing – namely microbial genome information from NCBI’s RefSeq database – but after that they are very different organisms.

* The UCSC Microbial Genome browser includes archaea, bacteria and archaeal virus genomes, and is based on a slightly modified version of the UCSC Genome Browser system, which is an amazingly powerful browser that we know and love here at OpenHelix. On their homepage they describe the resource as:

The UCSC Microbial Genome Browser is a window on the biology of more than 300 microbial species from Bacteria and Archaea domains. Basic gene annotaiton is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data, and soon, high-throughput RNA sequencing. Direct contributions of functional genomic data or bioinformatic analyses are welcome.

Information is presented as ‘tracks’ aligned along the sequence of the genome. These tracks can be hidden, expanded and customized to display exactly the information a researcher is interested in, in the exact format that the researcher would like it. The database contains hundreds of microbial genomes and information from these genomes can be retrieved and analyzed by intersecting datasets using UCSC’s powerful Table Browser resource. We have multiple free tutorials on the general UCSC Genome Browser which would be applicable to using the UCSC Microbial Browser.

* The UCSC Archaeal Genome Browser is another microbial resource based on the general UCSC Genome Browser & displays information very similarly to that of the UCSC Microbial Genome Browser, but the two offer differences in the information tracks and species available. We just created a full tutorial on this resource in July of this year & the homepage has been updated significantly since then, so this group must really be active! (Watch for an announcement of our updated tutorial in the near future…)

* The Integrated Microbial Genomes resource is from the Joint Genome Institute, and also obtains its sequences from NCBI’s RefSeq database, as well as from their own sequencing efforts. It contains sequence data on archaea, bacteria, eukaryotes (for comparative purposes), viruses and plasmids. To quote the IMG homepage:

The Integrated Microbial Genomes (IMG) system ( Nucleic Acids Research, 2010, Vol. 38) serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context…

… The IMG user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools.

However, rather than presenting vast amounts of information aligned along a sequence, this resource aims to provide researchers with the most state-of-the-art technology for microbial comparative analyses. They provide an array of tools for finding precise sets of genomes, genes of functions according to various characteristics. The researcher is then able to use Abundance profilers, functional alignment tools, analysis carts and more to compare the items within the set to one another. Visualizations present the comparative information beautifully and clearly, but are not flexible in the same way that UCSC browser displays are using the track controls.

* The Integrated Microbial Genomes with Microbiome samples (IMG/M) resource is a Data Management & Analysis System that is related to IMG (which I bet you guessed) that specializes in the unique issues surrounding metagenomic sequences. It currently contains metagenome data on 133 microbiomes, specialized tools for metagenomic analyses, and all of the IMG data for reference in comparisons.

* The Complete Microbial Resource, or CMR, from the J. Craig Venter Institute is another general microbial resource, with archaeal, bacterial, and viral genomes. Its genome browser and comparative functions put it somewhere between the UCSC Microbial Browser & IMG, but with a real emphasis on the ability to easily download lists of genes, evidence or genomic elements as well as sequences, etc. that result from you analyses.

* The Complete Microbial Genomes database is from NCBI and offers an extensive collection of data, resources and tools for prokaryotic genomic analysis. Data and tools are organized into three major tables, including Organism info, Complete genomes, and Genomes in progress. Sequence information is available for over 1000 archaeal and bacterial genomes and utilizes NCBI’s extensive resources to provide extensive linkout options to additional information. Complete Microbial Genomes is one of NCBI’s many Entrez Genome Projects.

These resources are just a few of the many general microbial resources publicly available to researchers. Then there are species specific resources such as EcoliHub, subject specific resources such as MiST (Microbial Signal Transduction Database), and resources associated with specific projects such as the Human Microbiome Project (HMP) resources: Data Analysis and Coordination Center (DACC) for the Human Microbiome Project (HMP), the NIH Human Microbiome Project (HMP) Roadmap Project, and the HMP NIH Intramural Skin Microbiome Consortium (NISMC) data at dbGaP, which Mary heard about at a recent meeting. I think I’ll leave exploration of these specialized projects to another day though.

References:
UCSC Microbial Genome Browser and UCSC Archaeal Browser:
Schneider, K. (2006). The UCSC Archaeal Genome Browser Nucleic Acids Research, 34 (90001) DOI: 10.1093/nar/gkj134

IMG:
Markowitz, V., Chen, I., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N., & Kyrpides, N. (2009). The integrated microbial genomes system: an expanding comparative analysis resource Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp887

IMG/M:
Markowitz, V., Ivanova, N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I., Grechkin, Y., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K., Hugenholtz, P., & Kyrpides, N. (2007). IMG/M: a data management and analysis system for metagenomes Nucleic Acids Research, 36 (Database) DOI: 10.1093/nar/gkm869

CMR:
Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O., & Sutton, G. (2009). The comprehensive microbial resource Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp912

Complete Microbial Genomes:
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., Feolo, M., Geer, L., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Mizrachi, I., Ostell, J., Panchenko, A., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., John Wilbur, W., Yaschenko, E., & Ye, J. (2009). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp967

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