Lecture 33 Flashcards
What is genomics?
The study of entire genomes, including the areas of:
Organisation and structure of genomes
Comparisons of genomes among organisms
interactions among genes within a genome
What is bioinformatics?
The management, organisation and analysis of large volumes of biological data to answer questions never anticipated by the investigator or data collector
What are the key differences between gene sequencing and genome sequencing?
Gene sequencing uses lab bench biology with PCR while genome sequencing uses automation and robots to give high throughput with computational processing of short sequence reads
What are the features of whole genome shotgun sequencing?
The sequencing is done first, mapping is done after this using the short sequences obtained
What is the process of genome shotgun sequencing?
Break the genome into random locations
Clone the randomly selected fragments
Sequence the clones (using primers that give overlapping sequence reads)
assemble these into contigs
Assemble contigs into scaffolds and use these to estimate the complete sequencing
What is a contig?
A segment of sequence obtained by overlapping two existing known segments
How is ordered clone sequencing done?
Mapping is done first then the sequence is obtained
Library is searched for sequenced clones with similarities in restriction enzyme recognition sequences
Overlaps are arranged to form a physical map
the minimal number of overlapping clones required to give the minimal tiling pathway is found
Those clones are then sequenced to allow assembly of the genome sequence
What is massively parallel sequencing?
New sequencing technologies that produce gigabases of data in very short times
These include the screening of genomes from several individuals, characterising the transcribed RNA in a cell and surveying the microorganisms in an environmental sample
What occurs on the computational side of pyrosequencing?
Converting the light sequences to DNA sequences is a major computational task
There is a relatively high error rate so it is critical to filter data and correct errors.
This is performed by a computer where it deletes unusually long or short reads
The largest known sequence is then aligned to a known genome
What are the four methods of finding genes?
Open reading frames, Statistical predictions, Expressed genes and codon usage
How do open reading frames help us find genes?
An open reading frame is the genomic region from an initiation point to the stop codon in prokaryotes (This method cannot be used in eukaryotes due to introns)
As the start codon may also code for an internal methionine the longest distance must be found
Important considerations in this method is that both strands need to be considered and each strand has 3 possible reading frames so there are 6 total possibilities
Open reading frames may overlap due to chance occurrence of initiation and STOP codons in other reading frames
How can statistical predictions be used to find genes?
Building a statistical model to describe gene features such as the location of exon/intron splice sites
This can then be applied to an unknown sequence to predict the locations of the feature. The model will give the probability or likelihood that the feature is at any particular location in the sequence
How can expressed genes be used to help find genes?
Exons can be identified through cDNA which when aligned with genomic DNA will reveal exons
Or expressed sequence tags which are fragments of mRNA in a cell type or tissue representing a part of the transcribed genome which will reveal the location of exons through alignment with genomic DNA
How can codon usage help find genes?
As there is degeneracy in the genetic code, not all codons for the same amino acid are used with equal frequency within genes
In this way a different frequency of the three base strings is expect in exons than seen in different reading frames or non-transcribed regions
How can gene function be predicted?
As there is shared ancestry among organisms we can use sequence comparisons to find shared genes, shared gene products, and shared gene functions
We can then make an inference of occurrence, location, function of a gene through comparison
