Bioinformatics

"Hey Rocky, watch me pull a rabbit out of my hat!" I realized that I should add just a bit more information to last answer on gene identification, so here it is. After the last installment, Diego commented:
but still you do not know exactly what part of your DNA sequence is matching to the annotated protein.
Ahh, but we do. And I was negligent in not showing you. There are multiple ways to view the GenBank record that we arrived at while ... Read more
Welcome back! If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the project here. And we had some rather curious results. It appeared that our sequence ... Read more
Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence, any sequence, from a set of 16 unknown sequences and use BLAST to identify that sequence. This ... Read more
Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil.i-dc4398c754d67d54c86378e8729b36bc-parallel_DNA.gif With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure. Yet here is, on the screen, parallel DNA. The image that I posted a couple of days ago came from this same structure. In that image ... Read more
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality. Later on, when the genome sequencing turned into a race, and the pace of DNA sequencing began to increase, some genome ... Read more
What do genetic testing and genealogy have in common? The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one. Another answer is that both tests can involve DNA sequence data. And that leads us to another question. If the sequence of my mitochondrial DNA is only two bases different from Cleopatra's, am I really a distant relative? And how do I really even know that my mitochondrial DNA is only two bases different in the first place? What does having a DNA sequence really mean? Students ... Read more

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