Biochemical Analysis Sequencing and Bioinformatics

Exam 2

Moore’s Law

An observation and projection of a historical
trend. Rather than a law of physics, it is
an empirical relationship linked to gains from
experience in production

genome projects involve the following three steps

1. assembly of individual sequence reads into larger contains and ultimately complete genome sequences

2. gene prediction and functional annotation based on protein and protein domain comparisons to established sequence databases

3. comparative sequence analysis of single genes, DNA fragments or entire genomes to explore gene functions and genome architectures

Genomics – Next Generation Sequencing (Needs)

• Quality assessment/control for
sequencing projects
• Technology development to improve
sequencing pipelines
• Development of
bioinformatics/computational tools to
improve sequencing pipelines or to
improve downstream sequence
analysis
• Management of individual sequencing
projects
• Informatics equipment
• Data analysis downstream of initial
data processing

genome assembly

the computational process of deciphering the sequence composition of the genetic material (DNA) within the cell of an organism, using numerous short sequences called reads derived from different portions of the target DNA as input

generate annotation

process of identifying
functional elements along the
sequence of a genome, thus
giving meaning to it

• necessary because the
  sequencing of DNA produces
  sequences of unknown
  function.

  
  
  

comparative sequence analysis

a powerful method for aiding human gene identification,
inferring function of a gene's product, and identifying novel
functional elements such as those involved in transcriptional
regulation

• comparing to different organisms

NCBI

anyone can submit

comparative genomics

a field of biological research in which the genomic features of different organisms are compared

genomic features

the DNA sequence, genes, gene order, regulatory sequences, and
other genomic structural landmarks

Two different approaches are commonly used in comparative genomics

1. Distantly related species are compared that share a specific phenotype.

2. Closely related species are compared that differ with respect to a specific phenotype.

WGS metagenomic sequence analyses include determination of the functional composition of a microbial community based on

• Protein domain families
• Gene Ontologies
• Antibiotic resistance