Changing your research field
I had long been a researcher in tissue engineering, not only one type of specific tissue but a mishmash of different organs or tissues, including bone, skin, neural and cartilage tissue engineering. Although I had thoroughly enjoyed my journey, I realised that I had enjoyed computational research the most. Do not listen to your current…
Tools for Life Scientists
In this post, you will find some great tools that I have been using since the beginning of my PhD. You may be familiar with most tools; but, I am sure you will find some tools that you have not heard before. Also, even the title mention “Life Scientists”, you will find some tools useful…
Right tool for productivity
Everyone I know either in academia or industry has one or two (or sometimes a mouthful) things to say about productivity. Some even say how productive they are. Yes, they are the ones to sacrifice their sleep to meet the deadlines. I am not one of those, nor will I be ever. If you are…
Enumerating k-mers Lexicographically
When cataloguing a collection of genetic strings, we should have an established system by which to organize them. The standard method is to organize strings as they would appear in a dictionary, so that “APPLE” precedes “APRON”, which in turn comes before “ARMOR”.
RNA Splicing
In “Transcribing DNA into RNA”, we mentioned that a strand of DNA is copied into a strand of RNA during transcription, but we neglected to mention how transcription is achieved. In the nucleus, an enzyme (i.e., a molecule that accelerates a chemical reaction) called RNA polymerase (RNAP) initiates transcription by breaking the bonds joining complementary…
Locating Restriction Sites
The war between viruses and bacteria has been waged for over a billion years. Viruses called bacteriophages (or simply phages) require a bacterial host to propagate, and so they must somehow infiltrate the bacterium; such deception can only be achieved if the phage understands the genetic framework underlying the bacterium’s cellular functions. The phage’s goal…
Calculating Protein Mass
In “Translating RNA into Protein”, we examined the translation of RNA into an amino acid chain for the construction of a protein. When two amino acids link together, they form a peptide bond, which releases a molecule of water. Thus, after a series of amino acids have been linked together into a polypeptide, every pair…
Enumerating Gene Orders
Point mutations can create changes in populations of organisms from the same species, but they lack the power to create and differentiate entire species. This more arduous work is left to larger mutations called genome rearrangements, which move around huge blocks of DNA. Rearrangements cause major genomic change, and most rearrangements are fatal or seriously…
Open Reading Frames
In “Transcribing DNA into RNA”, we discussed the transcription of DNA into RNA, and in “Translating RNA into Protein”, we examined the translation of RNA into a chain of amino acids for the construction of proteins. We can view these two processes as a single step in which we directly translate a DNA string into…
Inferring mRNA from Protein
When researchers discover a new protein, they would like to infer the strand of mRNA from which this protein could have been translated, thus allowing them to locate genes associated with this protein on the genome.
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Cenk Celik 