This week, I learned more about the specific topics we will be researching. To supplement my background in biology, I read Sean Eddy’s paper, “How do RNA folding algorithms work?” that was published in November 2004 in Nature Biotechno
Additionally, being we will be working with the programming language Perl for much of our research, I became more familiar with its syntax and semantics. To accomplish this, I created a program that opens any specified FASTA file, concatenates the (DNA/RNA/Protein) sequence of nucleotides or amino acids, and extracts substrings of length 5. The substrings are then stored in a hash along with the number of times they appear in the sequence. The output is a list of each substring along with the number of times it appears in the sequence. It also lists any unique substrings that were found. To test my program, I downloaded several complete (mainly viral) and partial genomes from the NCBI (National Center for Biotechnology Information) and found that the output was consistent with what I expected.
logy as well as abstracts from several other papers about RNA folding prediction. I also read a report done by a previous student that did research closely related to ours. Additionally, being we will be working with the programming language Perl for much of our research, I became more familiar with its syntax and semantics. To accomplish this, I created a program that opens any specified FASTA file, concatenates the (DNA/RNA/Protein) sequence of nucleotides or amino acids, and extracts substrings of length 5. The substrings are then stored in a hash along with the number of times they appear in the sequence. The output is a list of each substring along with the number of times it appears in the sequence. It also lists any unique substrings that were found. To test my program, I downloaded several complete (mainly viral) and partial genomes from the NCBI (National Center for Biotechnology Information) and found that the output was consistent with what I expected.