Bioinformatics Week 8

Next generation sequencing: Generates large amount of sequences. 
The price of sequencing has dropped significantly since the start of sequencing. 
454 Pyrosequecning

• DNA is broken into smaller sequences. 
• Attach single peice of DNA is attatched to a bead
• Single pieces of DNA on the beads are then applified
• Sequencing reactions occur and the sequencing data is created. 

Illumina Sequencing 

• DNA is broken into smaller sequences 
• Clusters of the DNA are created by adding adapters(stick together non congrous DNA)
• Clusters are amplified in PCR
• Then you sequence each individual cluster by adding in primers and nucleotides which are tagged with different colored florescences. 

The current sequencing technologies fall short in some aspects. First, they all break the DNA into smaller segments and then sequence them. So you are sequencing small parts and it's harder to see the bigger picture. You have to try to piece back together the small sequences to figure out what the whole piece of DNA was. When there are repetitive regions within DNA it becomes more complicated to piece back the DNA sequences once you have sequenced it. You don't know where these sequences were located on the DNA. Putting the sequences back together is called assembly. There are different programs which assemble the sequences (ABySS, SOAPdenovo, Velvet). When you are given an assembly you are also given an assembly score. This assembly score comes with the number of contigs (overlapping sequences). The fewer contigs the better. 

RNA-seq: Sequences mRNA. Can identify if alternative splicing events have occurred (removing introns, not removing introns, etc)

• DNA is broken into smaller sequences 
• Clusters of the DNA are created by adding adapters(stick together non congruous DNA)
• Sequence it 

Metagenomics: Studying the sequences of microbial organism in their natural environments by just taking samples of their environment (soil, water, etc) and then you sequence it using next generation sequencing. Before you would have to remove the organism from its natural environment and then culture it in an artificial lab environment which could alter your results.