BNFO 653 – Pattern Recognition and Gene Finding (2018)
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Projects: Computation to Solve Problems
The following projects guide you through a problem requiring computer programming for its solution. Choose whichever one (or more) that strikes your fancy. Better to do one well than try too many.
An example of data mining that combines a search of text with a search of protein sequences. STRs are commonly used in forensic application. Extracting useful insights from microarray data sliced by metabolic pathways. How to find them by repetitive structure, and how to compare their locations in different genomes. Using position-specific scoring matrices to extend experimental knowledge of the genomic targets of a certain DNA-binding protein to find new, previously unknown sites. Uses a well-studied cyanobacterial transcription factor as an example. Certain genes are known or suspected of being co-regulated. Perhaps the genes contain a common upstream sequence that is the target of a transcription factor. Uses a motif-finding program (Meme) to investigate, possible regulatory motifs in Streptococcus genes. A family of proteins does not show great sequence similarity, except within certain amino acid motifs. Can these motifs be used to find additional family members? Uses a plant protein involved in floral symmetry as an example. A hypergeometric derivative of the central tendency summed over all conjugate variables... huh? Scrap the statistics and play with a simulation of Mendel's experiment to get at the key question: Are the results likely to have arisen by chance or not? This is a somewhat more involved simulation, showing that computational simulation can sometimes take the place of statistical tests and can often shed light on what those tests are trying to do. Protein alignments can help you peer into the mind of Nature and see what parts of the proteins she considers important. In this tour, the object is to learn something about proteins from herpesviruses. |