Friday, June 13, 2014

pLOT v1.0.1 Update Release

  pLOT update to v1.0.1 is now available.  This update allows gaps to be part of sequences in your Annotations Library and search strings (amino acid and DNA versions).  This results in a more flexible search and auto-annotations than you would get using "N" or "X" as ambiguous DNA bases or amino acids respectively and allow matching of sequences with variable lengths.  Gaps are represented by a "-" for both DNA and amino acid sequences.  An importable Annotations Library add-on file is also available with a few sequences to demonstrate this.




Example
Lets look at a sample amino acid sequence.  Using the previous method and introducing ambiguous residues as "X" can match to similar sequences but only if the differences in their amino acid sequences are at the "X" AND if the number of amino acids in the proteins are the same.  If not, it will return a non-match as anything after an amino acid insertion or deletion would fail to match with the amino acid at the same number position of the search as shown below:

Search Sequence: MVDSSRRXWNKAGHAVRAIGRLSSP
Matches:              MVDSSRRKWNKAGHAVRAIGRLSSP
Won't Match:       MVDSSRRKWHNKAGHAVRAIGRLSSP

Using gaps in saved search sequences can increase the odds of finding variant matches. For example:

Search Sequence: MVDSSR-IGRLSSP
Matches:              MVDSSRRKWNKAGHAVRAIGRLSSP
Matches:              MVDSSRRKWNKAGHAVRARKWNKAGHAVRAIGRLSSP
Matches:              MVDSSRRKWHNKAGHAVRAIGRLSSP

Considerations

  • Keep sequences flanking a gap long enough to ensure low numbers of non-specific matches.  In the above example, the search string "MV-SP" would be a bad choice.
  • There may be times you want to specifically identify homodimers.  In these cases, it is useful to include the linking region in your search string.  For example, the fluorescent protein tdTomato (from Clontech) is a linked dimer of two identical GFP derivatives.  Using the search strings below, tdTomato will be identified as itself as well as a GFP-derivative but GFP will not be identified as tdTomato because the tdTomato string includes the linker region (underlined) not found in GFP.
    • GFP-derivative search string" XVSKGEE-GMDELYK"
    • tdTomato Search String        "XVSKGEE-HGTGSTGSGSSGTASSEDNNMA-GMDELYK"

If you do not already have v1.0 installed then download this
pLOT v1.0.1 Complete Installation File
(v1.0.1 has been replaced by 1.0.2b)
Use this if you'e installed v1.0, download this and copy the two files to your pLOT program directory
pLOT v1.0.1 Update
(v1.0.1 has been replaced by 1.0.2b)
Annotations Library Add-on.  Download and then import it from the Library Manager

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