Biology 1201A Chapter Notes - Chapter 16: Non-Coding Rna, Functional Genomics, Intron
Chapter 16:
Genomes and Proteomes
16.1 Genomics: An Overview
- Genomics: characterization of whole genomes including structure (sequence), function and
evolution
- Consist of 3 main areas of study.
1. Determination and annotation:
-obtaining complete sequences and analyzing to locate putative protein-coding and noncoding
RNA genes and other important sequences in genome.
2. Functional genomics:
-determining function of genes- using genome sequence data to study functions of genes and parts
of genome. For protein-coding genes, it includes determining what proteins they encode and how
they function in metabolic processes of organisms.
3. Study genomic evolution:
-comparing genome sequence data develop an understanding of how genes, particularly protein-
coding genes, originated and genes and genomes evolved
- Comparative Genomics: study of genome sequences for a number of organisms that represent an
16.2 Genome Sequence Determination and Annotation
- obtaining the sequence of bases in a genome using DNA sequencing techniques and analyzing the
data with computer based approaches
16.2a Genome Analysis Begins with DNA Sequencing
- Shotgun Sequencing: determine the sequence of a whole genome
o Genomic DNA broken into many overlapping fragments
o Each fragment amplified to produce copies, determining the sequence of fragments
o Computer forms a sequence based on the fragments
- DNA Sequencing Methods:
1. DNA Purification
2. DNA Fragmentation
3. Amplification of fragments
4. Sequencing by each fragment
5. Assembly of fragment sequences into genome sequences
16.2a Genome Sequences Are Annotated to Identify Genes and Other Sequences of Importance
- Annotation:
o Identification of functionally important features in the genome
o performed by researches in the field of bioinformatics- application of math and Comp.
Sci to extract info from biological data
- Open Reading Frames: (ORF)
o Span of codons from start to stop
o Usually protein-coding gene if longer than 100 codons
o Finding protein-coding ORF’s is simple in prokaryotic genomes- few genes have introns
o Eukaryotic protein-coding genes have introns so more sophisticated algorithms used to
identify genes. - Algorithms can search for:
▪ Junctions between exons and introns
Document Summary
Genomics: characterization of whole genomes including structure (sequence), function and evolution. Consist of 3 main areas of study: determination and annotation: Obtaining complete sequences and analyzing to locate putative protein-coding and noncoding. Rna genes and other important sequences in genome: functional genomics: Determining function of genes- using genome sequence data to study functions of genes and parts of genome. For protein-coding genes, it includes determining what proteins they encode and how they function in metabolic processes of organisms: study genomic evolution: Comparing genome sequence data develop an understanding of how genes, particularly protein- coding genes, originated and genes and genomes evolved. Comparative genomics: study of genome sequences for a number of organisms that represent an. 16. 2 genome sequence determination and annotation obtaining the sequence of bases in a genome using dna sequencing techniques and analyzing the data with computer based approaches.
