I’ve already written about mutation databases a few weeks back (you can read my post here), but there is a big group of variations I haven’t mentioned in my post. These variants are somatic mutations (if you’re not familiar with the main classes of mutations, check out this page). Very shortly: somatic variations are mutations that can occur in any cell of the body, except germ cells. Therefore, these mutations are not passed on to children. Specific kinds of somatic mutations can cause cancer or other diseases.
Month: September 2013
Flashcard Fridays – A night at the museum
If you’ve ever worked as a field biologist, you know how hard sample collection can be. It’s a tough job even if you only want to collect biological samples from a small number of animals living in a relatively confined area (I could tell you long stories about the two summers I spent catching lizards). If you want to get samples from a list of species which all live in different (and possibly exotic) locations you’re going to need an almost infinite amount of money, a big group of dedicated people and a decent amount of luck. Fortunately, we have an alternative: museums. Just to give you an idea: there are more than 126 million items in the collection of the National Museum of Natural History (Smithsonian) alone. So, what’s all this got to do with next generation sequencing?
Workflow Wednesdays – Coverage analysis 1.
Nowadays, when whole exome and whole genome alignments are becoming fairly routine and even gene panels often target hundreds of genes, it’s no longer a valid option for researchers to visually check the quality of alignments. Generating coverage measures and statistics is a good tool for identifying sequencing or alignment problems and therefore offers a great alternative for browsing through alignments.
Bioinformatics for Beginners – ROSALIND
The Rosalind project provides an opportunity for learning bioinformatics through problem solving. Rosalind works the following way:
- you select a problem to solve from a list of available problems,
- you look through the problem and work out your solution (an example input and output is provided for each problem),
- you download a random dataset and provide the output of your solution for that specific dataset,
- the output is then checked by the Rosalind system and you get feedback immediately.
Flashcard Fridays – NGS and cancer
The emergence of new sequencing technologies made it possible for researchers to dig deeper into complex genetics related subjects. One of these complex, hard-to-study, but extremely relevant subjects is cancer. Today”s articles provide a glimpse inside the world of cancer research with next generation sequencing:
