The DNA knows where the DNA comes from

We know that all cells in our bodies carry DNA in their nuclei. To a first order, all the DNA in our bodies is identical (As is normal with biology, there are exceptions, called chimeras which provide much material for the tabloids). However, we know that we are not homogenous blobs of cells of the …

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The marvelous bee odometer

You probably know that not only can bees compute the vector (direction and distance) to a discovered food source relative to their hive, but they can also convey this vector to their hive mates. Here, I'll talk a little bit about one component of this system - the Bee odometer: how do bees figure out …

CIGAR strings

When I first joined Seven Bridges my boss would be describing things and he would say "Do this with the CIGAR" or "compute that from the CIGAR". Reluctant to be found out so early I nodded sagely and made a furtive note in my notebook to check out what the heck a CIGAR was. You …

Use pysam

This is a plug for Pysam: a well designed and feature rich wrapper for HTSlib. I've used pysam for a few years now and it has gotten better with time. It is now a very efficient and convenient library for reading and writing BAM files, reading VCF, FASTQ and FASTA files. For VCF and FASTA …

Molecular combing

Molecular combing is a fun technique that is used to study longer stretches of DNA and quite different from the next generation sequencing by synthesis I've been exposed to. In this technique ┬áDNA is mechanically stretched out on a slide and then locations of interest are labeled using fluorescent compounds. One can then image the …

Seeing chromosomes

Did you know that chromosomes can be seen under a light microscope, and they get their name from the fact that they are strongly stained by certain colored dyes? I was reading through our government's collection of educational materials on genomics. Going through the history of the gene I was startled to learn that people …

The year humans lost a pair of chromosomes

Many mistakes in science persist because the creators of wrong knowledge refuse to acknowledge their mistakes and often intimidate others (with correct information) from positions of power. This phenomenon has lead a once well known practitioner of the trade to remark "Science advances one funeral at a time".