Genomics, Bioinformatics and Proteomics

Genomics

Study of genome

1. Structural

2. Functional

3. Comparative

4. Metagenomics

Structural genomics

Analyzing nucleotide sequences to identify genes and sequences

Whole genome sequencing

Shotgun cloning: the most widely used strategy for sequencing and assembling an entire genome

1. Genomic DNA is cut into fragments and contigs are made

2. Entire chromosome is assembled by computer program

3. Fragment are aligned based on identical DNA sequences

Contigs

Continous fragments

Overlapping fragments adjoining segments that collectively form one continous DNA molecule within chromosome

Bioinformatics

Uses computer based approaches to organize, share and analyze data related to: gene structure, gene sequence and expression, protein structure and function

Application of bioinformatics

1. Comparing DNA sequences

2. Finding gene-regulatory regions (promotors and enhancers)

3. Predicting amino acid sequences

4. Deducing evolutionary relationships between genes

5. Identifying: Protein structure and functions, Genes in genomic DNA sequences and Structural sequences (telomeres)

BLAST

Basic Local Alignment Search

Software application used to compare a segment of genomic DNA to sequences throughout major databases. Identifies portions that align with or are same as existing sequences

Open reading frames

ORFs, sequences of triplet nucleotides translated into amino acid sequence of a protein. Typically begin with initiation sequence (ATG) and end with termination sequence (TAA. TAG, TGA)

Functional genomics

Study of gene function based on resulting RNAs or possible proteins they encode as well as regulatory elements

Homologous genes

Genes that are evolutionarily related.

1. Orthologs: genes from different species thought to have descended from common ancestors

2. Paralogs: genes in same species

SNPs and CNVs

1. SNPs : Single nucleotide polymorphism, single base change in genome

2. CNVs : Copy number variation, segment of DNA duplicated or deleted

Encode

Encyclopedia of DNA elements,

Uses experimental approach and bioinformatics to identify and analyze functional elements that regulate expression of human genes

Comparative genomics

Compares genome of different organisms to answer questions about genetics and other aspects of biology.

Incorporates the study of gene and genomic evolution. Explores relationship between organisms and environment. Studies differences and similarities between organisms and how differences contribute to phenotype, life cycle and so on.

Metagenomics

Environmental genomics, use whole genome shotgun approach, to sequence the genome from entire communities of microbes in Environmental samples of water, air and soil

Transcriptome

Global analysis of gene expression.

Studies expression of genes by genome qualitatively and quantitatively.

1. Qualitively: identifies which genes are not expressed and which are

2. Quantitatively: measures varying levels of expression of different genes

Proteomics

Identification, characterization and quantitative analysis of proteins encoded by genome cell, tissue or organism

Used to reconcile differences between number of genes in genome and number of different proteins produced

Allows comparison of proteins in normal and diseaaed tissue

System biology

Incorporates data from genomics, transcriptomics proteomics and other areas of biology

Intepretes genomic information in context of structure, function and regulation