BIF501 Handouts by VUBuddy

BIF501 - Bioinformatics II

Applications of Bioinformatics

1. Drug Development
2. Crop Improvement
3. Microbial Genome
4. Gene Therapy
5. Biotechnology
6. Comparative Study
7. Evolutionary Studies
8. Veterinary Science
9. Molecular Medicine 10. Personalized Medicine 11. Preventive Medicine 12. Waste Cleanup 13. Antibiotic Resistance 14. Alternate Energy Science 15. Insect Resistance 16. Climate Change Studies 17. Nutritional Quality

Drug development

✓ Drugs target only about 500 proteins ✓ Disease mechanisms and using computational tools identify and validate new drug targets

Crop improvement

✓ Comparative genetics of the plant genomes ✓ Information obtained from the model crop systems can be used to suggest improvements to other food crops. ✓ At present the complete genomes of Arabidopsis thaliana (water cress) and Oryza sativa (rice) are available.

Microbial genome applications

✓ Complete genome sequences ✓ Environment, health, energy and industrial applications ✓ Isolation of the genes that give them their unique abilities to survive under

extreme conditions.

Gene Therapy

➢ Gene therapy-used to treat, cure or even prevent disease ➢ Clinical trials

Biotechnology

➢ Archaeoglobus fulgidus and Thermotoga maritima ➢ Corynebacterium glutamicum ➢ Xanthomonas campestris ➢ Lactococcus lactis

Evolutionary studies

➢ The sequencing of genomes from all three domains of life; eukaryota, bacteria and archaea

Farm animals including cows and sheep have been sequenced

➢ The human genome project ➢ 3000-4000 hereditary disease including Cystic Fibrosis and Huntingtons disease ➢ Response to an environmental stress causes cancers, heart disease, diabetes ➢ Human Genome Project Data Base

➢ Pharmacogenomics ➢ Sequence variants in DNA ➢ Trial and error to find the best drug ➢ Patient's genetic profile ➢ With the specific details of the genetic mechanisms of diseases being unraveled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. ➢ Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.

➢ Deinococcus radiodurans ➢ Potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals

➢ Enterococcus faecalis ➢ Virulence region-resistant genes ➢ The discovery of the region, known as a pathogenicity island

Alternative energy sources

➢ Chlorobium tepidum ➢ Capacity for generating energy from light

➢ Bacillus thuringiensis ➢ Control serious pests of cotton, maize and potatoes ➢ Insecticides can be reduced and hence the nutritional quality of the crops is increased

➢ Increasing levels of carbon dioxide emission-global climate change. ➢ Study the genomes of microbes that use carbon dioxide as their sole carbon source.

Improve nutritional quality

➢ Genes transferred into rice to increase levels of Vitamin A, iron and other micronutrients ➢ Reducing occurrences of blindness and anaemia

Topic -3 Nucleotide Sequence Databases

Biological Databases:

Biological databases in general store biological data and their main goals are

1. Data storage · 2. Information retrieval · 3. Knowledge discovery · Classification:

Biological databases can be classified as

➢ Primary databases (that stores the Primary Sequences) ➢ Secondary databases (the primary sequences are annotated and kept in Secondary Databases) ➢ Specialized Databases (they are dedicated towards some specific organism or can have some disease data)

Biological databases can also be classified on the bases of types of data which they contain, such as:

➢ Nucleotide databases · ➢ Protein databases · ➢ RNA databases · ➢ Genome databases

➢ Expression databases (Gene Expression Databases)

Issues:

The issues which are present generally in other databases are also found to be in Biological databases that may be co-related with the relatively slow pace of quality assurance techniques as compared to the pace with which new data is emerging, so the issues are similar and are as follows:

Due to limited Q/A

➢ Redundancy · ➢ Inconsistency · ➢ Incompatibility (format, terminology, data types, etc.) · Nucleotide Sequence databases:

The Nucleotide Sequence Databases are one of the types of Biological Databases that contains nucleotide sequences in it, which can be DNA and cDNA or EST sequences.

Here, we have a diagram where we have a genomic DNA which has different Exons(we know that in Eukaryotes, we have exons and introns). So exonsgets transcribed into mRNA and we can get cDNA from this mRNA through reverse transcriptionand then we can store this cDNA into our databases whereas the ESTs are the subsets within those cDNA’s.