sequence analysis

Yes, you can! Really, I thought this was going to be more challenging, but the nice folks at the NCBI have made a special personal genomics FTP site. You can also get Craig Venter's genome, and maybe even do some comparative genomics and see if one has a few deletions. After all, don't you want you find out who's is bigger? Oh, I can tell this is going to be fun! Get the traces at ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_GenomicsRead more
What do you do when base-callers disagree? Okay DNA sequencing community, I want your help with this one. One of these sequences was called by phred and the other by the ABI KB base calling program. Which one should I believe?

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Sometimes I open up files and do short experiments just because - well, I'm curious. And sometimes I immediately wish I hadn't done that because what I opened looks like a larger can of worms than I really want to see.
Many medical conditions today are treated but never cured. Imagine, a child with a genetic disease like juvenile diabetes or hemophilia. This child will be taking expensive medications for their entire lives. In the case of some diseases the cost of the medications might be more than child or their parents can ever hope to earn in their lifetimes, much less spend on a life-saving drug. This is one of the many reasons why people have placed such great hopes in gene therapy. If a disease results from a defective gene, and we could replace it or supplement it with a functional gene, ... Read more
Last week I found a bug in the new NCBI BLAST interface. Of course, I reported it to the NCBI help desk so it will probably get fixed sometime soon. But it occurred to me, especially after seeing people joke about whether computer science is really a science or not, that it might surprise people to learn how much of the scientific method goes into testing software and doing digital biology.

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What happens when the scientific method ... Read more
BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's very good at illustrating evolutionary relationships on a molecular level. A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I ... Read more
By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.

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Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated ... Read more
i-ba347d980e861564c774555d0a24afcf-phone.jpgIt was only a couple of weeks ago but it seems like years. I had spent a month learning how to use most of the features on my shiny new phone and we were in Alaska using Google maps to find our way around Fairbanks. My thumbs were getting sore, but so what? I could a give a slide show on my phone, I could read my Gmail messages, and we could find a friend's house in the Google map satellite ... Read more
How does grass grow in the extremely hot soils of Yellowstone National Park? Could a protein from a virus help plants handle global warming? Okay, that second sentence is wild speculation, but we will try to find the answer to our mystery by aligning our protein sequence to a sequence from a related structure.

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Read part I, part II, ... Read more
i-8295f915da92d0ca11a67cd144057d90-rhodies.jpgThe first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound- ... Read more

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How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues. Read part I, part II, part III, and part IV to see how we got here. And read onward ... Read more

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