Downloading the example data
The last base pair, the so-called WIKI:Wobble_base_pair, in a WIKI:Codon changes more frequently during evolution than the first and second base.
This will be demonstrated in this tutorial.
Please activate "Nucleotides" in the BUTTON:UserProfile#newButton()!.
The following nucleotide sequences need to be downloaded from NCBI:
WIKI:Proteasome alpha 1-subunits:
NCBI_NT:BC022354 NCBI_NT:M63641 NCBI_NT:NM_017283 NCBI_NT:NM_203782
NCBI_NT:XM_001139648 NCBI_NT:XM_001213840 NCBI_NT:XM_001263332 NCBI_NT:XM_749396
WIKI:Proteasome alpha 2-subunits:
NCBI_NT:BC002900 NCBI_NT:BC026768 NCBI_NT:AB013342 NCBI_NT:NM_001024441
NCBI_NT:NM_001090584 NCBI_NT:NM_001046879 NCBI_NT:NM_079604 NCBI_NT:NM_001035980
NCBI_NT:XM_628527 NCBI_NT:XM_950392
Using the dialog BUTTON:DialogFetchSRS! involves three steps:
- Copying (CTRL-C and CTRL-V) the IDs into the text field
- Highlighting the IDs
- Pressing the download LABEL:"ncbi"-button
- Loading the downloaded files into STRAP by pressing the LABEL:FilesFetchedFromServer#BUT_LAB_Load-button
You should now see the nucleotide sequences in the alignment pane.
Select "nucleotides" in the selector JCOMPONENT:StrapView#choiceShading()! in the tool-bar.
Aligning the nucleotide sequences
Align the nucleotide sequences by pressing the tool-button JCOMPONENT:StrapView#button(BUT_ALIGN)!.
Use the tool-bar button W to export the alignment file to your word processor.
Translating the nucleotides sequences:
Now we are going to translate the nucleotide sequences with the dialog
BUTTON:DialogGenbank!. After translation you will see amino acid sequences
in the alignment pane.
Aligning the amino acid sequences:
Align the amino acid sequences by pressing JCOMPONENT:StrapView#button(BUT_ALIGN)!.
After alignment export the alignment BUTTON:DialogExportAlignment!.
In the export dialog select nucleotides instead of amino acids.
The wobble base position is written in lower case and the first two
base positions are written in upper case.
The result should look like the figure below.
Discussion:
Now we compare the result of the alignment computation with nucleotide with the alignment computation with amino acids.
There are significant differences.
Computation from nucleotides, the three bases that belong to one WIKI:codon are sometimes separated by gaps.
In the WIKI:ClustalW output for amino acid sequences it can be seen that
the wobble base position (lower case) exhibits high variability
compared to the first and second nucleotide position (upper case).
Conclusion: Alignments computed with amino acid sequences are more reliable than with
nucleotide sequences.