sequence analysis:
Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example. Plus, since GAPDH is a highly conserved, it's a great...
Posted on May 8, 2008 7:36 PM • 3 Comments •
A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well. The April 25th version of Nature News reports (1) that two viruses, HPV...
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Posted on April 27, 2008 5:50 PM • 10 Comments •
Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington. We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases shortened and paraphrased....
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Posted on April 24, 2008 10:41 AM • 9 Comments •
One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my headphones,...
Posted on April 22, 2008 3:36 PM • 2 Comments •
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
Can you solve this puzzle?
Posted on April 11, 2008 8:23 AM • 0 Comments •
Is it real or is it April Fools?...
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Posted on April 1, 2008 8:18 AM • 3 Comments •
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....
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Posted on March 17, 2008 2:05 PM • 3 Comments •
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
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Posted on March 11, 2008 12:00 PM • 6 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
A quick video introduction to BLAST.
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Posted on February 12, 2008 8:14 AM • 13 Comments •
The New England Journal of Medicine published a study yesterday showing that small changes in the DNA in the long arm of chromosome 16 are associated with autism. I met a teenager with autism last summer, when I attended family night at the Seattle Park and Rec summer camp program for kids with special needs. It's a fantastic program. The...
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Posted on January 10, 2008 12:00 AM • 13 Comments •
In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes...
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Posted on December 19, 2007 9:13 AM • 0 Comments •
Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers....
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Posted on December 14, 2007 10:33 AM • 4 Comments •
If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed and origin of the animal. The university and the company...
Posted on December 6, 2007 1:00 AM • 2 Comments •
If we suspected a virgin birth, how could we prove it?
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Posted on December 3, 2007 9:00 AM • 13 Comments •
Drug stores branch out from pregnancy to paternity.
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Posted on November 26, 2007 12:07 PM • 12 Comments •
Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C. All of three reads were obtained by sequencing PCR products, generated with the same set of primers. The quality...
Posted on November 20, 2007 3:20 PM • 0 Comments •
Kind of like reading tea leaves, but more meaningful.
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Posted on November 19, 2007 10:10 AM • 10 Comments •
You too, can compare chimp and human DNA.
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Posted on November 16, 2007 8:51 AM • 0 Comments •
Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.
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Posted on November 15, 2007 9:09 AM • 4 Comments •
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used...
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Posted on November 14, 2007 4:04 PM • 9 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
Sequencing the dirt: see how it's done
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Posted on October 27, 2007 7:00 PM • 0 Comments •
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles....
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Posted on October 26, 2007 2:20 PM • 0 Comments •
Dying bees and DNA sequencing
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Posted on October 25, 2007 12:15 PM • 1 Comments •
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...
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Posted on October 24, 2007 4:05 PM • 0 Comments •
During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...
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Posted on September 7, 2007 8:43 AM • 5 Comments •
Adding the costs and doing the math.
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Posted on September 6, 2007 12:16 PM • 13 Comments •
If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...
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Posted on September 5, 2007 10:35 AM • 4 Comments •
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value....
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Posted on September 4, 2007 12:42 PM • 11 Comments •
Why the ABRF of course! I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university...
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Posted on August 25, 2007 5:30 PM • 0 Comments •
I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....
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Posted on August 24, 2007 6:44 PM • 4 Comments •
Calling all bases, how many are correct?
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Posted on August 21, 2007 8:25 AM • 6 Comments •
Developing "biological intuition" through case studies
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Posted on August 17, 2007 1:53 PM • 0 Comments •
Sometimes asking a question can be a mistake. Especially when your question leads to more questions and having to question things that you didn't want to question, and pretty soon you begin to regret ever opening the file and looking at the data and asking the question in the first place. Sigh. Take a deep breath. Yesterday through a twist...
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Posted on August 15, 2007 7:50 PM • 8 Comments •
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...
Posted on August 15, 2007 8:00 AM • 0 Comments •
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? tags: DNA sequencing, DNA , base-calling programs...
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Posted on August 14, 2007 1:16 PM • 10 Comments •
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...
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Posted on August 3, 2007 4:23 PM • 8 Comments •
Software testing and the scientific method.
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Posted on July 23, 2007 3:46 PM • 0 Comments •
Some things I like, some were surprises.
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Posted on July 16, 2007 12:13 PM • 19 Comments •
BLAST has gotten harder.
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Posted on July 12, 2007 1:39 PM • 4 Comments •
Viewing chromatogram trace files on iPhone.
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Posted on July 9, 2007 12:12 PM • 3 Comments •
Could a protein from a virus help plants handle global warming?
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Posted on June 1, 2007 9:15 AM • 0 Comments •
Assigned readings on BLAST and phylogenetics.
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Posted on May 29, 2007 9:19 AM • 0 Comments •
Through the Related Structures tab and what I found there.
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Posted on May 25, 2007 9:00 AM • 2 Comments •
How does grass grow in the hot, inhospitable soils of Yellowstone National Park?
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Posted on May 18, 2007 8:43 AM • 0 Comments •
How do plants grow at 65°C?
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Posted on February 21, 2007 6:19 AM • 2 Comments •
"Beware the Jabberwock, my son! The jaws that bite, the claws that catch! Beware the Jubjub bird, and shun The frumious Bandersnatch!" - from Jabberwocky, by Lewis Carroll I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins....
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Posted on February 8, 2007 3:17 PM • 1 Comments •
Yesterday, both Joshua and I wrote about grasses that grow in the unusually hot soil at Yellowstone National Park. Now, I knew that hot springs bacteria can tolerate high temperatures, but I was really surprised to learn that plants could....
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Posted on February 7, 2007 1:36 PM • 0 Comments •
Defining a biology term for scientists in other disciplines.
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Posted on February 2, 2007 2:23 PM • 6 Comments •
Chimeras invade the sequencing lab!
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Posted on February 1, 2007 6:01 PM • 0 Comments •
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too...
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Posted on January 10, 2007 11:21 PM • 4 Comments •
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?...
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Posted on December 22, 2006 8:00 AM • 0 Comments •
Who infected the children with HIV: Using the data to solve the puzzle.
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Posted on December 7, 2006 6:33 PM • 2 Comments •
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)?...
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Posted on October 10, 2006 11:41 AM • 0 Comments •
We went on an excursion last weekend to see the Dead Sea Scrolls at the Pacific Science Center. None of us could resist going downtown to look at written texts over 2000 years old. Uncovered in 1946, by a Bedouin shepherd, the scrolls have had an interesting history over the past 50 years, most of it out of the public...
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Posted on September 27, 2006 8:59 AM • 0 Comments •
Razib inspired me to share some of the story behind why white people are considered derivatives. Reposted from the Classic Digital Bio. No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1)....
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Posted on September 26, 2006 8:58 AM • 3 Comments •
No biology course is complete these days without learning how to do a BLAST search. Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key. Development of the tutorial and the activity were supported by funding from the National Science Foundation. This is...
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Posted on September 7, 2006 9:59 AM • 0 Comments •
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. We also learn something about the people who did the experiment....
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Posted on September 1, 2006 11:37 AM • 0 Comments •
Like biology, all bioinformatics is based on the idea that living things shared a common ancestor. I have posted, and will post other articles that test that notion, but for the moment, we're going to use that idea as a starting point in today's quest. If we agree that we have a common ancestor, then we can use that idea...
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Posted on August 25, 2006 8:10 AM • 2 Comments •
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out....
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Posted on August 23, 2006 10:06 AM • 0 Comments •
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share...
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Posted on August 21, 2006 10:00 AM • 0 Comments •
Let the experiment begin....
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Posted on August 19, 2006 11:35 AM • 0 Comments •
The past few Fridays, we've been comparing human mitochondrial DNA with the mitochondrial DNA of different apes. We started doing this here, where you can find directions for getting started. And, we've found some interesting things....
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Posted on August 18, 2006 3:43 PM • 2 Comments •
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide...
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Posted on August 17, 2006 11:59 AM • 2 Comments •
During these past couple of weeks, we've been comparing mitochondrial DNA sequences from humans and great apes, in order to see how similar the sequences are. Last week, I got distracted by finding a copy of a human mitochondrial genome, that somehow got out of a mitochondria, and got stuck right inside of chromosome 17! The existence of this extra...
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Posted on August 11, 2006 1:14 PM • 5 Comments •
It's hard sometimes when you're out of synch with the rest of the world. While my fellow ScienceBloggers have been obsessing about breasts, I've been really amused by the genetics of ear wax. Eh, what's that you say? Yes, it's true. Back in March, when Nature Genetics published this paper from Yoshiura (and friends), this bit of fun just went...
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Posted on August 10, 2006 2:30 PM • 3 Comments •
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
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Posted on August 4, 2006 1:39 PM • 3 Comments •
We've had a good time in the past few last weeks, identifying unknown sequences and learning our way around a GenBank nucleotide record. To some people, it seems that this is all there is to doing digital biology. They would, of course, be wrong. We can do much, much more than identifying DNA sequences and obtaining crucial information, like who...
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Posted on July 28, 2006 8:00 AM • 0 Comments •
One of my favorite experiments, in our biotech program at Seattle Central Community College, was when my students sequenced promoters that they had cloned from E. coli . I liked this activity because it pulled lots of pieces together and allowed the students to connect the dots between the DNA sequences that regulate gene expression, the DNA sequences that code...
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Posted on July 25, 2006 8:00 AM • 0 Comments •
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ecosystems, isolate DNA, amplify...
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Posted on July 24, 2006 9:20 PM • 0 Comments •
"Hey Rocky, watch me pull a rabbit out of my hat!" I realized that I should add just a bit more information to last answer on gene identification, so here it is. After the last installment, Diego commented: but still you do not know exactly what part of your DNA sequence is matching to the annotated protein....
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Posted on July 21, 2006 7:26 PM • 1 Comments •
Welcome back! If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the project here. And we had...
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Posted on July 21, 2006 4:19 PM • 3 Comments •
Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence,...
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Posted on July 14, 2006 11:35 AM • 3 Comments •
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality....
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Posted on July 10, 2006 3:00 PM • 0 Comments •
My colleagues have come up will all kinds of interesting bloggy things to use as an excuse for Friday celebrations. Adventures in Ethics and Science has Friday Sprog Blogging for cute stories about her kids. A Blog Around the Clock considers Friday's the perfect day to write about weird sex. Pharyngula salutes the spineless with Friday Cephalopods. Good Math, Bad...
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Posted on July 7, 2006 9:00 AM • 2 Comments •
What do genetic testing and genealogy have in common? The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one. Another answer is that both tests can involve DNA sequence data. And that leads us to another question. If the sequence of my mitochondrial DNA is only...
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Posted on July 5, 2006 7:00 AM • 2 Comments •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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