Bioinformatics

A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind of database these days and I've discovered that it's really helpful to know something about SQL. Even a tiny bit of SQL, like "SELECT * from table" goes a long, long way. This revelation didn't happen overnight and when I ... 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

How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the conversation turns to Woody, and someone asks the question that no one wants to touch. Does Arlo's girlfriend know about Huntington's? ...dead silence... Now, I did see the movie ... 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

'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

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 plots that I refer to are ... Read more

Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data analyst or bioinformatics technician does in a DNA diagnostics company. As you might imagine, looking at every single DNA sample by eye gets rather tiring. One of the things that informatics companies ( ... Read more

As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration. Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue our analysis. I wrote this activity, in part, because of this awful handout that my oldest daughter brought home last year. She presented me with an overly photocopied paper that showed ... Read more

DNA sequence traces are often used in cases where:

1. We want to identify the source of the nucleic acid.
2. We want to detect drug-resistant variants of human immune deficiency virus.
3. We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the best dose of a therapeutic drug.

In the future, these assays will likely rely more on automation. Currently, (at least outside of genome centers) many of these results are assessed by human technicians in clinical research labs, or DNA testing ... Read more