Molecular Online Lab Summary
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  • This is the lab template: The context is a biological context based on a real biological problem. And a given hypothesisI don’t use computer science, strong word.When you read this template, you have a different view than an informatician.You want to understand the process to build the used tools.The architecture of the systemThe algorithm implementationThe quality of the resulting dataAnd so on

Molecular Online Lab Summary Presentation Transcript

  • 1. . Molecular online tools and server 16 Context Biological HypothesisStatement of problem / Case study: The FXN gene provides instructions for making a protein called frataxin. This protein is found in cells throughout the body, with the highest levels in the heart, spinal cord, liver, pancreas, and muscles. The Reduced expression of frataxin is theprotein is used for voluntary movement (skeletal muscles). Within cells, frataxin is found in energy-producing structures called mitochondria. Although its function is not fully understood, frataxin appears to help assemble cause of Friedrichs ataxia (FRDA), aclusters of iron and sulfur molecules that are critical for the function of many proteins, including those needed for energy production. Mutations in the FXN gene cause Friedreich ataxia. Friedreich ataxia is a genetic lethal neurodegenerative disease, howcondition that affects the nervous system and causes movement problems. Most people with Friedreich ataxia begin to experience the signs and symptoms of the disorder around puberty. about liver cancer? 0. Specification & aims Resolution process Aim: T1. Genome exploration: The purpose of this experiment is to initiate online Objective: used of Ensembl online tools to localize the FXN on the human genome and biological exploration tools of the human genome. We identify the genes implicate in pancreatic cancer disease. After, getting an appropriate simulated the application (FXN gene and pancreatic data (sequence) on FASTA and Blast format. cancer). Now we can understand how a researcher can come to identify cross biological knowledge available T1.1. Locate a given gene on human genome in data banks. T1.2. Get a genomic sequence from NCBI Keywords: T1.3. Get the protein information and sequence from EBI Bio: FXN, Frataxin, pancreatic cancer, CDKN4 T1.4. Save the export sequences data in data folder Math: HMM, Informatics: programing, bioinformatics tools, getting T2. Sequences manipulation and exporting data Objective: Find similar sequence using BLAST tools and make an alignment on given FXN on chromosome 9 Frataxin molecule structure (pymol) sequences. T2.1. Find similar sequences using BLAST tool T2.2. Align generated sequences with ClustalW tool T1.3. Visualized result using phylogenic tree on Jalview Biological DB ? T3. Bioextract server Objective: used server tool to optimized data manipulation process, apply on Bioextract server. Tools T3.1. Server Initialization T3.2. Pancreatic cancer & Frataxin (FXN) T3.3. Mapping, Alignment Pancreas anatomy Pancreatic cancer T3.4. Workflow save & reused Acquired skills Online and server tools: - Query biological DB (fasta, Html, txt, figure formats) Conclusion: ? - Sequence tools (protein and gene) Mapping (tmap) Alignment (clustalw2) - Manage data result (select, keep, map, export) - Built and reuse workflow 16 Korean Bioinformation Center, 2010 1