Bioinformatics or B101nformatics

One of my projects for the master was to investigate using data of the TCGA project. We (my teammates and me) decided to use data of the thyroid. We aimed to discover the reasons why women suffer more thyroid carcinoma than men. Distribution of samples of the TCGA dataset from the thyroid, separated by sex I don't want to repeat all the information on the report we did, you can find the work we did, you can find everything here .  The summary of the study is: Papillary Thyroid Carcinoma (PTC) is the most common type of thyroid cancer (Agrawal et al. 2014). It is more prevalent in women than men and its common diagnosis occurs between 25 and 65 years old (The Cancer Genome Atlas Accessed: 2016-06-1). The aim of our project is to study differentially expressed genes between tumor and normal samples taking into account whether there could be a gender effect on the tumorgenesis of PTC. Using data from the The Cancer Genome Atlas (Accessed: 2016-06-1) we have performed a diffe...

Do you ever heard about hexamer likelihood used to determine if a sequence is coding or not? In one of my assigments on my master of Bioinformatics there was a project to use hexamers instead. The hexamers are defined with 6 nucleotides on a sequence. The idea behind using hexamers is considering that in coding regions there is an influence of the previous codon to the next codon, whereas on the intronic or non-coding regions there isn't. The script works need three fasta files, the first one with intronic sequences, the second one with coding sequences, and the last one with sequences to analyze. All files must use the IUPAC code for sequences, and on the right frame. This is due to the way of signaling in which frame a sequence should be, which varies between programs and descriptions. It is also more difficult to calculate the best score for the unknown sequence, without presenting two scores or biasing for a training set. Assuming everything is on frame is safer and easi...