Bioformatics Flashcards
What does Bioformatics Mean ?
Using computer to study the concept of biology
Use of computational technique
The science of collecting and analysing complex biological data such as genetic codes.
Bioinformatics is the study of the flow of genetic/biological information
What is Genomics?
Genomics deals with databases and understanding the arrangement of genes and their expression; i.e transcription, mRNA, tRNA etc..
What is Proteomics ?
Proteomics is understanding all the proteins in each cell of an organism; subset of proteins represented in each tissue and at different stages of development and how they vary with disease
What does Structural Genomics deal with ?
Structural genomics deals with determining a representative 3-Dimensional (3D) protein structure of every protein family in the human genome; leverage human genome; various interactions
What are the computional goals of Bioformatics ?
Learn & Generalize: Discover conserved patterns (models) of sequences, structures, interactions, metabolism & chemistries from well-studied examples.
Prediction: Infer function or structure of newly sequenced genes, genomes, proteins or proteomes from these generalisations.
Organise & Integrate: Develop a systematic and genomic approach to molecular interactions, metabolism, cell signaling, gene expression
Simulate: Model gene expression, gene regulation, protein folding, protein-protein interaction, protein-ligand binding, catalytic function, metabolism…
Engineer: Construct novel organisms or novel functions or novel disease phenotype.
Gene Therapy: Target specific genes, or mutations, to change a disease phenotype.
LPOSEG
What type is Bioformatics ?
In silico
computer/algorithm-based experiments)
Program an algorithmn to help piece together structure and function of protein
How is Bioformatics used ?
Bioinformatics is used to help “focus” the experiments of the benchtop biologist.
One goal is to eliminate false positives that can waste time and money pursuing false leads.
Bioinformatics is not going to replace lab work anytime soon
In vitro/in vivo experimental proof is still the “Gold Standard”.
When Processing information what does Bioformatics require ?
Databases: Lists/banks of information
Algorithm: Defined step-by-step procedure for calculations.
In mathematics, computer science, and related subjects, an algorithm (derived from the name of an Iranian mathematician al-Khwārizmī) is an effective method for solving a problem expressed as a finite sequence of steps.
Algorithms needed to handle large and complex biological information.
What can Bioformatics do ?
Store derived information
Large databases of information (sequences)
Large databases of publications
Analyze stored information. E.g. molecular sequences (genome, transcriptome, proteome)
Identify structures
Look for patterns, similarities, matches
Challenges in Understanding Genetic Information
Genetic information is redundant
Different genes can encode the same proteins
Structural information is redundant
Different proteins have the same structure, fold
Genes and proteins are meta-stable
Border line of denaturing, losing structure
Single genes have multiple functions
Genes are one dimensional but function depends on three-dimensional structure
What occured in the 1960s ?
1960s: the birth of bioinformatics
Margaret Oakley Dayhoff created:
The first protein database
The first program for sequence assembly
