Bioinformatics

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 ... Read more

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. You may be wondering, and rightly so: just what is a SNP?

Never fear, hopefully this post will answer some of those questions.

SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a sequence of bases, and other people will have a different base at that position. The two forms of SNP are called "alleles." (Usually there are two forms, but that's ... Read more

"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. Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your ... Read more

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. So, last week I suggested that you, dear readers, go and find out why. I gave you a ... Read more

If you've read the previous posts on this topic, here and here, you're probably aware by now that I have this weird (okay, maybe fanatical) obsession with data. Or at least, with knowing if my data are right so I can get on with life, do the analysis and figure out the results. My results from last week suggested that re-processing chromatogram data (from the ABI 3730) ... Read more

I'll continue with the remaining parts of my career series shortly, but for the time being, I want to bring your attention to a really good post on doing bioinformatics as a software professional, and some commentary on the question that never seems to go away: "do biologists need to be able to program?" Thanks to GenomeWeb.

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From Paolo Nuin, we have a ... Read more

One time I was watching a football game on TV and they had a short quiz, called "You make the call" or something like that, and you had to watch a play and pretend to be a referee. A short video clip showed football players falling over each other. Then you were three possible calls that a refereee might make and asked to chose which was correct. After the commercial, the announcer would tell you which choice was right and explain why it was correct. I suppose this was a trick to make us watch the commercials, but I thought the game was kind of fun. My SciBling "Mike the Mad" had a great ... Read more

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 of fate, I ended up taking a look at the DNA sequences produced by two different base calling programs from the same chromatogram file, from an ABI 3730 DNA sequencing instrument. I thought they would be the same, or at least similar.

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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.