DNA sequence databases

Question 1

Purpose of DNA sequence databases

Answer 1

• Once you have a sequence of DNA, need to determine the function
• DNA sequence databases are repositories of all DNA & RNA sequences that have been generated

e. g. Genbank (USA), DNA database of Japan, Embolabs (Germany)
- all repositories exchange data w/ each other on regular basis

Question 2

Proteins in Databases

• putative
• To find out protein function

Answer 2

• Databases do have protein sequences w/in them
  
  • in many cases the protein is putative (means RNA could potentially code for a protein, but it hasn’t yet been verified)
  • Swisspot = database for verified protein sequences

To find out what a protein does, need to compare it to sequences w/in database to find most similar
-done via BLAST search (Basic Local Alignment Sequence Tool)

Question 3

Other things you can find out by a sequence

Answer 3

Can find motifs in sequences such as;

• DNA binding
• phosphorylation
• DNAases
• these are functional motifs - tell us more about what the protein is likely to do
• restriction sites in sequence
• amino acid codon preference (diff. species have diff. preferences for a.a. codons0

Question 4

Consequences of different species having codon preferences

Answer 4

1. Limits what genes we can transfer between species (if we don’t use codon that matches, we won’t have charged tRNA)
2. Detecting transfer of genes between species (genes transfer between species - found to be quite common)

*by looking at codon preference, can get info as to species of origin of transferred DNA

Question 5

Identification of species using sequencing

Answer 5

• Most frequent use = identification of species
  
  • more efficient than trying to grow on agar (only approx 3% of microbial organisms in soil grow on agar)
• sequence of 50 bp is sufficient to identify a species
• Can also use PCR
• usually ribosomal RNA ITS regions are used
  
  • ITS = Internal transcribed spaces - no known function but useful in phyogenetics & taxonomy

Question 6

How sequencing properly identified Oomycetes

Answer 6

Oomycetes = v. damaging plant patho-organism
-Previously classifed as fungi, but wasn’t responding to traditional fungi dealing methods

• was successfully reclassified used sequence
• understanding correct taxanomic placement is essential to understanding the biology