Bioinformatics Week 1

Bioinformatics is the study of data and the creation of algorithms and statistics to analyze them.

Three sub disciplines of bioinformatics:

• Creation of algorithms and statistics to sort data
• The analyzation and interpretation of the sorting
• The implementation of what you have learned in the sorting process

Bioinformatics started with Gregor Mendel and now continues with the mapping of organisms genomes.

Bioinformatics includes

Protein structure information, Dna information, gene information, patient information, clinical trial information as well as information about the metabolic pathways of many species.

Bioinformatics can be used to simulate cell environments which can help custom design drugs and personalize medicine. It can be used to create a better model of drug testing and replace the mouse. We have collected all this information about the human genome and other organisms however we have too much to analyze it manually, so we must create algorithms and programs that will analyze the database for us or at least organize it into a digestible portion. In terms of agriculture, bioinformatics can map the genome of plants and diseases that plague plants create plants that are resistant. GMO’s. Also resistant to droughts.

Bioinformatic tools must be developed around

• DNA sequence which determines protein sequence
• Protein sequence which determines protein structure
• Protein structure which determines protein function

Computational biologists use the tools and systems that bioinformaticians create to solve biological problems by creating algorithms and theories on how to utilize them.

Bioinformaticist knows how to create the systems and how to use them and make it easier for others to use them, a bioinformatician only knows how to create the system.

There are primary databases which contain data and then there are secondary databases which contain analyzation of that data.

What data systems already exist

Nucleotide sequence database

Collection of research publications and medical journals

3D structures of proteins

Organism classification: BIODIVERSITY largely unmapped and no set data base for it, all on paper

Enzymes and their function

Important technical abilities

JAVA

PERL: String manipulation

Regular expression matching

File parsing

Data format interconversion

FASTA format: represents nucleotide or peptide sequences in which base pairs are represented in single letter codes. Series of lines that should not exceed 120 characters and are usually 80 characters long.

Possible topic for project

*The structure of pathogens and their connection to the structure of functioning protiens in the human body. Or structure of pathogens against other pathogens.