view only residues with a consensus score lower than threshold

Jalview Discussion
1

Hi

I am a new user of jalview. I am using the program to inspect/edit a nucleotide alignment of about 188000 bp. The sequences that I’m inspecting are all at the intraspecific level so most of my alignment is identical. I wish to inspect those residues for which there is some evidence of variation. Is there a way to view only those residues with a consensus score less than a certain threshold.

Also as an aside, this is my first time using the list serve. I didn’t see a way to search old archives other than to click on the digest month by month and manually read through the list of headings. Can someone please tell me how to search for particular topics so I can avoid posting redundant questions?

Thanks

2

Hi Julie - thanks for your questions. I'll answer them in reverse :slight_smile:

Also as an aside, this is my first time using the list serve. I didn't see a way to search old archives other than to click on the digest month by month and manually read through the list of headings. Can someone please tell me how to search for particular topics so I can avoid posting redundant questions?

Great question. Google indexes our mailing list, so I just created a custom search link:
https://www.google.co.uk/cse/publicurl?cx=005718409729431308369:evyfdt8zyyq
I'll add a search box to the web site when I get a moment !

I am a new user of jalview. I am using the program to inspect/edit a nucleotide alignment of about 188000 bp. The sequences that I'm inspecting are all at the intraspecific level so most of my alignment is identical. I wish to inspect those residues for which there is some evidence of variation. Is there a way to view only those residues with a consensus score less than a certain threshold.

You've discovered something that really needs to be included in Jalview, but we haven't actually done yet :slight_smile:
I'm hoping we'll add the 'mark unconserved' function in a future release, but until then, you could use this groovy script:

// hides columns above a certain percentage identity threshold
// Open the Tools->Groovy Console
// paste the following lines in and
// press 'CTRL+R' or 'CMD+R' to execute

// percentage below which columns will be marked
def consThresh = 50f;

def alf = Jalview.getAlignframes();
for (ala in alf)
{
   // ala is an jalview.gui.AlignFrame object
   // get the alignment consensus annotation
   def alcons = ala.viewport.getAlignmentConsensusAnnotation();
   // and mark columns in a column selection object
   jalview.datamodel.ColumnSelection cs = ala.viewport.getColumnSelection();
   if (cs == null) {
     cs = new jalview.datamodel.ColumnSelection();
     ala.viewport.setColumnSelection(cs);
   } else {
     cs.clear();
   }
   int p=0;
   for (q in alcons.annotations)
   {
      if (q!=null && q.value<consThresh) { cs.addElement(p); }
     p++
   }
   // lastly simulate a 'SHIFT+CTRL+H' to hide unmarked regions
   ala.hideAllButSelection_actionPerformed(null);
}
// end of groovy script

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On 10/11/2014 14:11, Julie Lee-Yaw wrote: