sequence analysis

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. I have always known that DNA sequencing errors occur. This is why people build tools for measuring the error rate and why quality measurements are so useful for determining which data to use and which data to ... Read more
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 genes (It's not perfect, at least one of these genes is a ribosomal RNA methyltransferase and not a 16S ribosomal RNA.) ... Read more
Here's a fun puzzler for you to figure out. The blast graph is here:
i-02f5f2aaa95bc8ab8660ebaba090a49e-graph.png
The table with scores is here, click the table to see a bigger image: ... Read more
yep, I've become a videoblogger, at least sometimes. See the first video below. Be kind in the comments, this is a new thing for me. This video introduces the different blast programs, discusses word size, and how blastn works, the blastn score and the E value. The treatment is light and not too in depth, but as I said, it's an introduction. ... Read more
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-60b957fad1b9e1a3e306d0c520e02043-kids_singing.jpgI 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 kids spend a week or more at summer camp ... Read more
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 even a day later, is a different database. And, if you query a different database, you may get a different result. The series that I'm currently posting is one that I started working on a couple of years ago. ... Read more
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. DAG made me clarify my question by asking what I meant by "similarity." I was wondering whether I would be likely to find a statistically relevant match by doing a BLAST search and I hadn't really thought about the cutoff values. I decided to guess and say that that the protein would be about 30% similar and the nucleic acid about 60 ... Read more
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 said meat traceability is necessary to ensure consumer safety, particularly in cases of infectious disease outbreaks or accidental feed contamination.
No more ... Read more
i-e3899186ef576991098fed4ff62eab0f-small_dice.gif'Tis the holiday season and, according to ancient lore, the time when miraculous events are most likely to take place. One of those well-known and miraculous events of ancient days was the birth of a son to a young girl, who, although she was married (Okay, I'm not sure about this part of the story) she was said to be a virgin and the birth to be a miracle. Hmmm. ... Read more
GenomeWeb reports that Rite Aid drug stores on the West coast are now selling kits for doing paternity tests. The kits are made by Sorenson Genomics in Utah. Sorenson Genomics calls it the "peace-mind-test." Really! Each kit contains a swab for collecting cheek cells from the inside of your mouth and a container for mailing the sample to the lab. As far as I can tell, you buy the kit for $29.99, take a sample, fill out the consent forms, and ... Read more

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