Bioinformatics has replaced old fashioned labs, saving time and money
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Databases
Primary - DNA sequences
Secondary - results of analysis
This information allows for the creation of cloud web servers such as GenBank, EBI-EMBLE and DDBJ. These companies exchange data daily.
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Protein sequences
Protein sequences are stored as 1 letter codes, The sequenese fold to form structufe. there are now over 100,000 structures. Programs can now predict and visualise molecules.
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Next Generation Sequencing
Identify genes and predict structures
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BLAST
Complete structures:
name
protein sequences
protein function & structure
Unknown/ incomplete structures:
similar structure
common ancestors
BLAST is commonly used to repidly compare new structures
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GeneCards
Used to discover more abount genes.
Location
Function
Expression
Similar proteins
Disease relationships
Literature
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Ensemble
A common genome browser. Primary sequences are used to calculate or predict protein infromation simple characteristics such as weight. Sexondary sequences are used to indentify patterns, related proteins and enzyme active sites.
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Comparing protein Sequences
Used to compare how sequences changes during evolution.
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Sequence Alighment
Databases line up sequences to identify similar features in colums
Not aligned
Aligned
Alternnative alignments
Examples ClustalW2 and Cluster Omega
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Applications of Bioinformatics
Determining sequences - shotgun sequencing
Copy DNA lots of times
Chop up the copies
Assemble fragments when they overlap
Meaning from genome sequence - gene annotation
Where are the genes
What do they do
This is done rapidly and on a large scale
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Functional Annotation
You need a large number of proteins, from this you can predict 3D structures
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Genome Sequences
Sequences from a single genome are useful for descovering
Nessesities of life
Control economically important traits of crops
Personalised medicine
Only 1% of our genes have not been found in other species.
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1000 Genomes Project
An extensive cataogue of genetic variation
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Drug discovery
It costs on average $800 million to develop a drug. All currently marketed drugs target around 500 gene products, Bioinformatocs can help to evaulate new potential targets and antibiotics. This information is easily accessed by pharamceutical companies. When designing a drug there are programs which "dock" together the proteins and drugs, this is done through high-throughput screeing.
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