Practical
Steps to sequencing a DNA sequence:
1. Go to https://www.ncbi.nlm.nih.gov/
2. Click on the Basic Local Alignment Search Tool (BLAST) tab
Different types of BLASTs:
Nucleotide BLAST takes a nucleotide sequence and compares it to all
nucleotide sequences in the NCBI database.
Protein BLAST takes an amino acid sequence and compares it to all amino
acid sequences in the database
BLASTx takes a nucleotide sequence, converts it to amino acid sequence
and compares this to all predicted amino acid sequences in the database.
tBLASTn takes an amino acid sequence and compares it to DNA sequences
which are translated to amino acid sequences.
Each of these has advantages, depending on what you want to do. If I have a DNA
sequence, I normally start with a BLASTx because amino acid sequences tend to
change less frequently than DNA sequences and so comparisons between
sequences from different species are easier. This is because some amino acids are
encoded by several different codons so the DNA sequence can change without
altering the amino acid sequence of the protein.
3. Copy and paste the DNA sequence into the BLASTx input box A.
4. Once it has been processed, you will see what protein the gene encodes for.
If you look at the sequences below the top sequence you will see other sequences
for the same gene, but from other plant species.
5. If you click on the link to one of the proteins you will be shown the comparison of the
inputted sequence with the protein sequence in the database.
Examining restriction enzymes of a DNA sequence:
1. Go to http://nc2.neb.com/NEBcutter2/
2. Copy and paste your sequence in the input box and click submit. Once the
submitted, the page will generate a diagram showing all restriction enzymes that cut
once in the sequence. If you click the link to 2 cutters it will show a diagram of all
the restriction enzymes that cut twice in the sequence.
3. The grey bar on top shows how many amino acids are in the sequence
Biotechnology 1
, 4. Stop codons are underlined (highlighted in yellow and red font) in the sequence. But
the position of a stop codon can be calculated by multiplying the number of amino
acids in a sequence by 3.
5. All the sequence downstream (to the right) of the stop codon is known as the
untranslated region (UTR) as it does NOT encode for protein.
History of Biotechnology
“bios” – life
“technikos” – tools
“logos” – the study of
Biotechnology = the use of organisms, using some technical process, to the
advantage of mankind and the environment.
Biotechnology 2
,Biotechnology 3
, Impacts of biotechnology:
Reduction in pesticides
Increase in yields
Increase in farmer income
Uses of biotechnology:
Produce food/increase yield
Medicine
Biofuel
Stem cell research
DNA fingerprinting
Biotechnology 4
Steps to sequencing a DNA sequence:
1. Go to https://www.ncbi.nlm.nih.gov/
2. Click on the Basic Local Alignment Search Tool (BLAST) tab
Different types of BLASTs:
Nucleotide BLAST takes a nucleotide sequence and compares it to all
nucleotide sequences in the NCBI database.
Protein BLAST takes an amino acid sequence and compares it to all amino
acid sequences in the database
BLASTx takes a nucleotide sequence, converts it to amino acid sequence
and compares this to all predicted amino acid sequences in the database.
tBLASTn takes an amino acid sequence and compares it to DNA sequences
which are translated to amino acid sequences.
Each of these has advantages, depending on what you want to do. If I have a DNA
sequence, I normally start with a BLASTx because amino acid sequences tend to
change less frequently than DNA sequences and so comparisons between
sequences from different species are easier. This is because some amino acids are
encoded by several different codons so the DNA sequence can change without
altering the amino acid sequence of the protein.
3. Copy and paste the DNA sequence into the BLASTx input box A.
4. Once it has been processed, you will see what protein the gene encodes for.
If you look at the sequences below the top sequence you will see other sequences
for the same gene, but from other plant species.
5. If you click on the link to one of the proteins you will be shown the comparison of the
inputted sequence with the protein sequence in the database.
Examining restriction enzymes of a DNA sequence:
1. Go to http://nc2.neb.com/NEBcutter2/
2. Copy and paste your sequence in the input box and click submit. Once the
submitted, the page will generate a diagram showing all restriction enzymes that cut
once in the sequence. If you click the link to 2 cutters it will show a diagram of all
the restriction enzymes that cut twice in the sequence.
3. The grey bar on top shows how many amino acids are in the sequence
Biotechnology 1
, 4. Stop codons are underlined (highlighted in yellow and red font) in the sequence. But
the position of a stop codon can be calculated by multiplying the number of amino
acids in a sequence by 3.
5. All the sequence downstream (to the right) of the stop codon is known as the
untranslated region (UTR) as it does NOT encode for protein.
History of Biotechnology
“bios” – life
“technikos” – tools
“logos” – the study of
Biotechnology = the use of organisms, using some technical process, to the
advantage of mankind and the environment.
Biotechnology 2
,Biotechnology 3
, Impacts of biotechnology:
Reduction in pesticides
Increase in yields
Increase in farmer income
Uses of biotechnology:
Produce food/increase yield
Medicine
Biofuel
Stem cell research
DNA fingerprinting
Biotechnology 4
