Tag Archives: IGB

Video Tip of the Week: IGB, Integrated Genome Browser

Recently in a paper we are working on we were asked to cover a bit more about various styles or types of genome browsers that are available. And the timing was perfect, because I had just revisited the information about IGB (Ig-bee) in their recent webinar series.

Announced on Biostar recently was this nice introduction to the new version: Live tour of new features in Integrated Genome Browser 8. Although I missed the live webinar, you can catch various recordings from their YouTube channel. I watched the intro one, but it doesn’t seem to be available right now (I’ve asked for a new link over at Biostar). It was a nice overview of the site, with an introduction to their setup and basic features. I’m hoping that it will re-appear soon. In the meantime, their YouTube page offers a few other ways to get started with IGB. Here’s one video, but there are several other quick-start style ones.

One of the key aspects was this nice way for groups to collaborate on evaluation and annotation of their data:

IGB makes it easy for groups to distribute and share their new genome assemblies and annotations. Using IBG’s simple QuickLoad system, you can share your new genome with collaborators, keeping the data private until published, and then use the same method to share the data with the world.

And there’s a lot more you can do. But that should give you a sense of the utility.

I played with IGB’s current version, and found it very flexible and useful. I may have overburdened it by asking for all those restriction sites, but they eventually loaded. I also loaded up some of the UCSC Genome Browser external data. You’d have to be familiar with the names of the data sets you’d want from UCSC beforehand though–a trip through our Table Browser tutorial might help you to understand that aspect a bit better.  But sometimes the big public genome browser sites won’t have all the flexibility and customization that you want for your explorations–and adding a browser like IGB to your repertoire could really help you to get precisely what you need in your data analysis projects.

Quick links:

IGB site: http://bioviz.org/igb/

YouTube channel with more videos: IGB Channel

Reference:

Nicol J.W., Helt G.A., Blanchard S.G., Raja A. & Loraine A.E. (2009). The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets, Bioinformatics, 25 (20) 2730-2731. DOI:

Announcement of Updated Tutorial Materials: UniProt, Overview of Genome Browsers, and World Tour of Resources

As many of you know, OpenHelix specializes in helping people access and utilize the gold mine of public bioscience data in order to further research.  One of the ways that we do this is by creating materials to train people – researchers, clinicians, librarians, and anyone interested in science - on where to find data they are interested in, and how to access data at particular public databases and data repositories. We’ve got over 100 such tutorials on everything from PubMed to the Functional Glycomics Gateway (more on that later).

In addition creating these tutorials, we also spend a lot of time to keep them accurate and up-to-date. This can be a challenge, especially when lots of databases or resources all have major releases around the same time. Our team continually assesses and updates our materials and in this post I am happy to announce recently released updates to three of our tutorials: UniProt, World Tour, and Overview of Genome Browsers.

Our Introductory UniProt tutorial shows users how to: perform text searches at UniProt for relevant protein information, search with sequences as a starting point, understand the different types of UniProt records, and create multi-sequence alignments from protein records using Clustal.

Our Overview of Genome Browsers introduces users to introduce Ensembl, Map Viewer, UCSC Genome Browser, the Integrated Microbial Genomes (IMG) browser, and to the GBrowse software system. We also touch on WebGBrowse, JBrowse, the Integrative Genomics Viewer (IGV), the ARGO Genome Browser, the Integrated Genome Browser (IGB)GAGGLE, and the Circular Genome Viewer, or CGView.

Our World Tour of Genomics Resources is free and accessible without registration. It includes a tour of example resources, organized by categories such as Algorithms and Analysis tools, expression resources, genome browsers (both Eukaryotic and Prokaryotic/Microbial) , Literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation. This main discussion will then lead into a discussion of how to find resources with the free OpenHelix Resource Search Portal, followed by learning to use resources with OpenHelix tutorials, and a discussion of additional methods of learning about resources.

Quick Links:

OpenHelix Introductory UniProt tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=77

OpenHelix Overview to Genome Browsers tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=65

Free OpenHelix World Tour of Genomics Resources tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=119

 


“What’s the Answer?” Thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:
With the advent of NGS data, lots of people have been looking for ways to visualize the BAM and SAM files for further analysis. We’ve been coming across that a lot in our workshops lately. I think you might be able to do that pretty well with a custom track at UCSC Genome Browser, though it’s probably not as simple as some tools listed and sometimes you need more. Today’s biostar question and answer:

…I want to know is there any freely available software for the visualization of the aligned reads including their sequences for Bowtie output (sam or bam format)….

Highlighted Answer:
The most up-voted answer was a simple one sentence:

See this great blog post reviewing several NGS genome viewers (they all read BAM format).

(It is a great blog post). There are other answers too that were helpful, check out the discussion…

Can you spare a genome browser?

Recently I’ve been coming across more and more requests and need for genome annotation and visualization software. Genomes are being completed left and right and researchers need ways to browse and annotate these genomes. There are a lot of tools out there. This post is a quick attempt to start listing those. It is not exhaustive right now, right now there are the ones off the top of my head and those focused a bit on visualization (though there is annotation). I plan to expand this list (have any to suggest) and enhance it with more descriptions as time goes forward. Probably make it a page if it becomes useful enough. I’m not listing databases (such as UCSC Genome Browser, RGD, Ensembl, Flybase, but rather software that researchers can use to create such browsable genomes). So, here we go…

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