Computational biology and genomics
I have written about sequence conservation in vertebrates previously but without much elaboration, hence I’m writing another post on this topic. An assumption of sequence conservation is that regions that show conservation, are under purifying selection, i.e. alleles that decrease the fitness of an organism are removed, and therefore probably do something important. Protein-coding regions…
Updated 2018 November 7th I wrote this post back in 2013 with the goal of finding a tool that can output a list of motifs within my sequence of interest. Five years later, I think the easiest tool for performing this task is HOMER. Being the huge Simpsons fan that I am, I’m surprised I…
The process of transcription, is influenced by the interaction of proteins called transcription factors (TFs) that bind to specific sites called Transcription Factor Binding Sites (TFBSs), which are proximal or distal to a transcription starting site. TFs generally have distinct binding preferences towards specific TFBSs, however TFs can tolerate variations in the target TFBS. Thus…
Updated 2013 October 4th. Recently I’ve been looking into transcription factor binding site analyses. With my mind set on this, I thought I’ll brush up this old post. MEME is a tool for discovering motifs in a group of related DNA or protein sequences. As a discovery tool, it is able to find de novo…