Bioinformatics Workshop

 We started by discussing what bioinformatics is and how it is used  We learned that DNA is the information about an organism  It is used in the process of protein creation  DNA  RNA  protein  There are three ways DNA can be translated into proteins  We extracted DNA from fruits.  This only worked in some fruits. It did not work for grapes and raspberries.  We also learned how DNA is extracted and analyzed in a lab setting.  We made necklaces by translating the genetic sequence of an organism into colored beads.

 On Day 2, we installed Bio-Linux on our computers. Bio-Linux is an operating system based on linux.  Later, we had an introduction to using linux commands and programming in perl.  We learned how to use the print statement, how to create and use variables, and how to get user input.

 We went to the NCBI website to get the genetic sequence of an organism, then we used BLAST to search for similar organisms. We saw the relative similarity of each organism based on its genetic sequence.  After that, we learned how to use EMBOSS commands in the command line. EMBOSS has a database of genetic sequences and has several functions to use them.  Examples: Retrieve Sequence, Translate Sequence, Reverse Sequence

 We spent the afternoon of the third day becoming more familiar with perl. We learned more commands for manipulating variables and conditional statements. We also learned how to loop through a program instead of going through it step by step. Finally, I wrote a program to find all the primes between two numbers given by a user.

 Yesterday, we learned what our project would be for the next two days. Our goal was to find two sets of primers that would differentiate two types of bacteria.  We selected two different types of bacteria; one that only lived in a human mouth and another that only lived in the lower gastrointestinal tract of a human.  We retrieved the sequences of three species of bacteria for each type and found a consensus of the genetic code for each of them. We made primers for each of them based on the consensus. Then, we used a program to find the five best forward and reverse primers for the collective genetic sequences of the bacteria.