sequence analysis

Have you ever wondered what kinds of viruses can be found in human waste? Mya Breitbart and team have been sequencing nucleic acids from fecal samples in order to find out. You might expect that we'd find viruses that infect humans or viruses that infect the bacteria in our gut. I wouldn't have expected to learn the result that they found. A large number, 60% of the viral DNA sequences were from unknown viruses. That's not a surprise. The surprise came when they looked at the RNA viruses.
Instead, the viral sequences most often came from a plant pathogen ... Read more
I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials. Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly. They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done ... Read more
I got my copy of "A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As soon I skimmed through it and read some of the questions and answers, I knew this would be the kind of quick reference that I would like to have sitting above my desk. Scherer has compiled a wonderful text that not only answers many of the kinds of questions that I can think to ask about the human ... Read more
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 model for looking at ... Read more
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 (Human papilloma virus) and measles virus, have been found in lung tumors. From Nature News:
Samuel Ariad of the Soroka Medical Center in Beer Sheva, Israel, and his colleagues began by analyzing ... Read more
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. The room in Kane Hall at the UW was already warm when we arrived last night (yes, I do go to evening seminars). A student handed us cards and cute little pencils for writing our questions and we sat down. We fought the impulse to write "What's the air ... Read more
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, and I get to listen to someone tell me about their work for an hour and show slides over the web. It's nice. Our company is even going to be involved in two webinars in the next two months. One of us is giving an Illumina webinar tomorrow ... Read more
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 ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes. Now, in one of our last projects we are determining where ... Read more
I know some of you enjoy looking at data and seeing if you can figure out what's going on. For this Friday's puzzler, I'm going to send you to FinchTalk, our company blog, to take a look at lots of data from a resequencing experiment that was done to look for SNPs and count alleles. The graph is at the end of the post. The graph shows data from 4608 reads (sequenced from both strands, forward and reverse). And there are some interesting patterns. Can you figure them out? Read more
Is it real or is it April Fools? The March 21st issue of Science has an interesting news article by Elizabeth Pennisi and a letter to the editor about a proposal to wikify GenBank. Currently, the NCBI holds the original authors responsible for editing or correcting entries and this does cause problems when those authors fail to return to the scene and fix what they've submitted. Some researchers are suggesting that third parties be allowed to fix some of those mistakes or at least add comments to records, to warn the unwary. There are some good arguments on both sides and it' ... Read more

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