1. . Molecular online tools and server 16
Context Biological Hypothesis
Statement 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 the
protein 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 Friedrich's ataxia (FRDA), a
clusters 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, how
condition 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