13377908
Description
| Question | Answer |
| How has the amount of data changed over time? | Grown exponentially |
| What should we do with all of the databases? | Have a database for the databases |
| Give an example of a database for databases | Metabase - a wiki for biological databases |
| List the 3 things needed in a database | 1. Archive of information 2. A schema 3. Tools to access the data |
| What is a schema? | A description of how information is organised |
| What is the 3rd type of nucleic acid called? | PNA - Peptide Nucleic Acid |
| Is PNA natural or synthetic | Synthetic |
| Give one example of a primary database | Genbank |
| What type of data is found in a primary database and where does it come from? | DNA and protein sequence Primary experiments |
| What kind of information can a primary database show? | Nucleic acid and protein structure Protein expression pathways Interactions / regulatory networks |
| What is a sequence motif? | The characteristic 'signature patterns' of protein families |
| Give an example of a signature of a protein family | Active binding sites for ATPases |
| Give an example of a derived database | Pubmed Metabase |
| What happens when a database doesn't have access tools? | They become data graveyards |
| What should database structure be based on? | The likely queries NOT the 'natural organisation' |
| What is string matching and what can you use to do it? | Find similar sequences in a database when given a nucleic/amino acid sequence BLAST |
| What is shape matching and what can you use to do it? | Find similar structures in a database when given a peptide/protein structure DALI server |
| Give 2 main problems of bioinformatic databases | Given sequence of unknown protein - can't find similar structures Given structure of protein, can't find similar sequences |
| Some databases use hand curation and others automated, give one example of each | Hand curated - OMIM Automated curation - Uniprot |
| Are quality control checks automated or manual? | Manual |
| What do quality control checks do? | Remove other genomes E.g. Mycoplasma |
| Why is the internet really useful for databases? | Makes them more accessible |
| What kind of classification is used? | Linnean (from 18th century) Additional levels e.g. sub-phylum |
| What is the method of classification (starts with Kingdom) | Kingdom-Domain-Phylum-Class-Order-Family-Genus-Species |
| How were the 3 domains of life found? | 1977 Carl Woese Used 16s ribosomal RNA to build a tree of life |
| What are the 3 domains of life? | Bacteria - Eukarya - Archea |
| What can you do to help identify evolutionary relationships? | Compare more sequences (the more compared the easier) |
| What enables the ordering of phylogenetic events? | Retrotransposon insertions E.g. SINES and LINES |
| What is PSI-BLAST? | Position Specific Iterative (see flowchart for more details) |
| Give an example of when PSI-BLAST was useful | PAX-6 human sequence, used PSI to search for distant orthologues Showed to be orthologous with 'eyeless' mutant in drosophila |
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