Tag Archives: genomics resources

Restriction sites in your sequences

A question we get asked all the time–and I see on mailings lists with about a twice/year frequency–is where can I look at the restriction sites in my sequences? I’m going to mention a few that I know about, but if anyone has other favorite tools or spots, do let us know in the comments.

UCSC Genome Browser: if you look in the browser in the “Mapping and Sequencing” Track groups area there is a menu called Restr Enzymes. I have turned this track on, and turned off some other default tracks, and created a “Session” to show you exactly how this can look. I picked a small gene for the example. Load my session: http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Mary%20Mangan&hgS_otherUserSessionName=restriction_enzymes

You can see the sites in Ensembl, too. From that UCSC session I provided you can click the link in the blue navigation area at the top of the UCSC page to go to the exact same region in Ensembl. In the “Detailed View” section at Ensembl you can see menus for “Decorations” and other display features. In Decorations you can check the box for Rest. Enzymes to see them on your viewer.
plasmapper.jpg
However, there may be times where your sequences is different from genomic, or not available in a species browser, and sometimes you just want another type of viewer. You might try PlasMapper (http://wishart.biology.ualberta.ca/PlasMapper). I took the same sequence from the browsers (the Casp-1 gene) and put the FASTA sequence in, and created a really quick map. It also gives text output if you prefer. It can add a display for some handy features that you might have on plasmids or constructs like promoters or affinity tags. Takes only a few seconds, a very handy little freely available tool for you to know about. I know it isn’t new, but it is such a common question for us that we thought we would mention it.

Dong, X., Stothard, P., Forsythe, I.J., Wishart, D.S. (2004). PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Research, 32(Web Server), W660-W664. DOI: 10.1093/nar/gkh410

Rat Genome Database requests signatures: by Thursday

rgd_logo.jpgA call came from RGD this week across their mailing list. They are doing a “white paper” to accompany a group of research papers are coming out in Nature Genetics. You can read the paper and become a signatory on this paper, demonstrating your support for rat genome research. There is a podcast right on their homepage that explains this in more detail.

If you think you might like to show your support as a signatory, please:

1. Go over to the RGD homepage. Listen to the podcast. (Ignore that dreadful music at the beginning, it goes away).

2. Download and read the white paper that is there. If you can support it, email the team.

3. Put your requested information (name, title, affiliation, etc) in an email to Tim and Howard–their address are right below the podcast.

If you think others in your department would be interested, please mail out a call to them. The RGD team needs this by Thursday February 28.

EDIT: bumped back up because today is the deadline.

What's your problem? Open Thread

q_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

What's Your Problem? Open Thread

q_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

TE insertions in genomes

transposon graphicIn the recent database issue of NAR, there are two reports of transposable element (TE) databases. I already discussed one in an earlier post. That one is a database that includes Gypsy elements (non-LTR retroposons) and retroviruses and aims to be a database “devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements.” Hopefully to develop into a database of all TE’s. The other paper, by Levy et al. (“TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates“)1, I’ll discus briefly here introduces a somewhat different database of transposable elements.

ResearchBlogging.orgAs the paper discusses, TE’s have been implicated in a large number of effects on the vertebrate genome: affecting expression and “contributing to genetic diversity, genomic expansion, genomic content and genomic rearrangements.” Whether these immense changes are the raison d’être for transposable elements or the byproduct of a parasitic DNA element, I’ll leave for discussion (though I would side with the latter), but they are unarguably major factors in genome evolution and don’t fit the definition of “junk DNA.” :D.

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What's Your Problem? Open Thread

question_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk.  If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Transposon Database

ResearchBlogging.orgI started my Ph.D. studies into the evolution of non-LTR retrotransposable elements in 1990 and found the world of mobile genetic elements or transposons (aka a long time ago… jumping genes) to be varied, complicated and fascinating. In 1993 I discovered the web. I’ve hoped for and searched for a database of these “Mobile genetic elements [that] are self-contained genomic units capable of proliferating within their host genomes”1 to little satisfaction. Such databases exist such as the Mouse Transposon Insertion Database and the dbRIP (human retrotransposon polymorphisms in humans) and several others. But these almost entirely organism-specific databases. This helps the study of the organism (mobile elements have an effect on the genome), but little in the study of transposons as a class.

So, I was happy to see the latest article in the NAR database issue on GypDB

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Sponsored Genomics Resource Tutorials, available again

Our server went down last week and the host provider had to move our server. The settings weren’t completely corrected, so if you have attempted to view the free tutorials and training materials this week, you might have had problems doing so.

We have fixed that problem and those links now work. Please visit our tutorials!

As a reminder, here are the tutorials that are sponsored by providers and free to the user:

GeneSNPs
sponsored by the National Institute of Environmental Health Sciences (NIEHS)

Genome Variation Server (GVS)
sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington

Integrated Microbial Genomes (IMG)
sponsored by the Joint Genome Institute

SeattleSNPs
sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington

UCSC Genome Browser (Intro and Advanced Topics)
sponsored by the University of California Santa Cruz Bioinformatics Group

VISTA Comparative Genomics Tools
sponsored by Lawrence Berkeley National Laboratory

What's your problem? Open Thread

blue_key_qmark.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, chime in.

The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.