@*~RSC_HELP_TUTORIAL_WOBBLEBASE
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.
The following nucleotide sequences need to be downloaded from NCBI:
WIKI:Proteasome alpha 1-subunits:
GB:BC022354 GB:M63641 GB:NM_017283 GB:NM_203782
GB:XM_001139648 GB:XM_001213840 GB:XM_001263332 GB:XM_749396
WIKI:Proteasome alpha 2-subunits:
GB:BC002900 GB:BC026768 GB:AB013342 GB:NM_001024441
GB:NM_001090584 GB:NM_001046879 GB:NM_079604 GB:NM_001035980
GB:XM_628527 GB:XM_950392
Using the dialog HTMLDOC_BUTTON:BUT_C1(DialogFetchSRS)! requires three steps:
- Copying (Ctrl+C anld Ctrl+V) the IDs into the text field
- Highlighting the IDs
- Pressing the download NCBI-button
- Loading the downloaded files into STRAP by pressing HTMLDOC_BUTTON:SBUTS_TAB_FETCH_PDB_Load
You should now see the nucleotide sequences in the alignment pane.
Select "nucleotides" in the selector HTMLDOC_JCOMPONENT:HTMLDOC_JC_Strap_comboColorScheme! in the tool-bar.
Aligning the nucleotide sequences
Align the nucleotide sequences by pressing the tool-button HTMLDOC_BUTTON:SBUT_ALIGN!.
Keep a copy of the current alignment by exporting the current alignment.
Translating the nucleotides sequences:
Now we are going to translate the nucleotide sequences with the dialog
HTMLDOC_BUTTON:BUT_C1(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 HTMLDOC_BUTTON:SBUT_ALIGN!.
After alignment export the alignment HTMLDOC_BUTTON:BUT_C1(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.
WIKI:codon are sometimes disrupted 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.
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