Resolution process

Context

0. Specification & aims

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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 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 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 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.

Molecular online tools and server 16

Keywords: Bio: FXN, Frataxin, pancreatic cancer, CDKN4Math: HMM, Informatics: programing, bioinformatics tools, getting and exporting data

16 Korean Bioinformation Center, 2010

Conclusion: ?

Reduced expression of frataxin is the cause of Friedrich's ataxia (FRDA), a lethal neurodegenerative disease, how about liver cancer?

Aim: The purpose of this experiment is to initiate online biological exploration tools of the human genome. We simulated the application (FXN gene and pancreatic cancer). Now we can understand how a researcher can come to identify cross biological knowledge available in data banks.

T1. Genome exploration: Objective: used of Ensembl online tools to localize the FXN on the human genome and identify the genes implicate in pancreatic cancer disease. After, getting an appropriate data (sequence) on FASTA and Blast format.

T2. Sequences manipulation Objective: Find similar sequence using BLAST tools and make an alignment

on given sequences.

Acquired skillsOnline and server tools:- Query biological DB (fasta, Html, txt, figure formats)- Sequence tools (protein and gene) Mapping (tmap) Alignment (clustalw2)- Manage data result (select, keep, map, export)- Built and reuse workflow

Biological Hypothesis

FXN on chromosome 9Frataxin molecule structure (pymol)

Pancreatic cancer

Pancreas anatomy

?

Bio

log

ical

DB

Tools

T1.1. Locate a given gene on human genomeT1.2. Get a genomic sequence from NCBI T1.3. Get the protein information and sequence from EBI T1.4. Save the export sequences data in data folder

T2.1. Find similar sequences using BLAST toolT2.2. Align generated sequences with ClustalW toolT1.3. Visualized result using phylogenic tree on Jalview

T3. Bioextract serverObjective: used server tool to optimized data manipulation process, apply on Bioextract server.

T3.1. Server Initialization T3.2. Pancreatic cancer & Frataxin (FXN) T3.3. Mapping, Alignment T3.4. Workflow save & reused

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