SP scores in JalView?

Hi Jim,

This is almost too trivial to ask, but can JalView calculate SP scores (and similar alignment statistics)? There is an option 'Extract scores...' in the Calculate menu, but that does not appear to do anything when I use it.

(I must admit I'm still on 2.8...)

···

--
Groetjes,

Anton
  _____________ _______________________________________________________

            > >
_ _ ___,| K. Anton Feenstra |
/ \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands |
\_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
            > Feenstra@few.vu.nl - www.few.vu.nl/~feenstra/ |
            > "Move about like a Scientist, lay down, get kissed" |
            > (Red Hot Chili Peppars) |
_____________|_______________________________________________________|

Hi Anton,
Pardon me if I’m duplicating a previous answer, but I didn’t see one…

There are various scores available via the AACon web service connected to Jalview as described here:
<http://www.jalview.org/help/html/webServices/AACon.html>

The Valdar paper cited in that page describes the options in more detail. Some of the scores are SP or very SP-like. I don’t recall seeing sub-options in the AACon dialog, so for some of these it may not be obvious which substituation matrix is used. The Valdar paper is here:
<http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/full>

Since I’m a Chimera person, I’ll also plug that program (very briefly, I know this is the JalView list!). Chimera can calculate sum-of-pairs conservation via the embedded AL2CO method, and you have your choice of a dozen or so different substitution matrices and what proportion of gaps are tolerated in a column. It can’t handle as large alignments as JalView can, however. The conservation values are easily/automatically mapped to any structures associated with the alignment. Tutorial example:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1>

Best,
Elaine

···

-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 7, 2014, at 7:47 AM, Anton Feenstra <k.a.feenstra@vu.nl> wrote:

Hi Jim,

This is almost too trivial to ask, but can JalView calculate SP scores
(and similar alignment statistics)? There is an option 'Extract
scores...' in the Calculate menu, but that does not appear to do
anything when I use it.

(I must admit I'm still on 2.8...)

--
Groetjes,

Anton
_____________ _______________________________________________________
> > >
> _ _ ___,| K. Anton Feenstra |
> / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
>( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands |
> \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
> > Feenstra@few.vu.nl - www.few.vu.nl/~feenstra/ |
> > "Move about like a Scientist, lay down, get kissed" |
> > (Red Hot Chili Peppars) |
>_____________|_______________________________________________________|
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Thanks, I'll look into that!

Jim, I basically need some scoring to compare alignments produced by different tools/settings. Preferably, I'd use several scores so as not to be dependent on one. Initially, it is just for students in a practical, (starting tomorrow), but it is also a recurring use case for my own research. Directing them to a webserver or even the jalview console would work fine for this purpose.

Pretty as JalView is, sometimes you just don't want to visually compare all alternative alignments you may have for a particular dataset ;-O

···

On 08-11-14 23:38, Elaine Meng wrote:

Hi Anton,
Pardon me if I’m duplicating a previous answer, but I didn’t see one…

There are various scores available via the AACon web service connected to Jalview as described here:
<http://www.jalview.org/help/html/webServices/AACon.html>

The Valdar paper cited in that page describes the options in more detail. Some of the scores are SP or very SP-like. I don’t recall seeing sub-options in the AACon dialog, so for some of these it may not be obvious which substituation matrix is used. The Valdar paper is here:
<http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/full>

Since I’m a Chimera person, I’ll also plug that program (very briefly, I know this is the JalView list!). Chimera can calculate sum-of-pairs conservation via the embedded AL2CO method, and you have your choice of a dozen or so different substitution matrices and what proportion of gaps are tolerated in a column. It can’t handle as large alignments as JalView can, however. The conservation values are easily/automatically mapped to any structures associated with the alignment. Tutorial example:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1>

--
Groetjes,

Anton
  _____________ _______________________________________________________

            > >
_ _ ___,| K. Anton Feenstra |
/ \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
( | )| | | De Boelelaan 1081 - 1081 HV Amsterdam - Netherlands |
\_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
            > Feenstra@few.vu.nl - www.few.vu.nl/~feenstra/ |
            > "Move about like a Scientist, lay down, get kissed" |
            > (Red Hot Chili Peppars) |
_____________|_______________________________________________________|

Hi Anton,
The AACon scores I mentioned before show up directly in the JalView window, below the sequence alignment. You call that calculation directly from the JalView menu; it’s all connected:
<http://www.jalview.org/help/html/webServices/AACon.html>

I also forgot to mention before that the JalView alignment quality score that also shows up below the alignment automatically (you don’t need to call AACon) is also very similar to an SP score, as described in the JalView manual:
<http://www.jalview.org/help/html/calculations/quality.html>

Best,
Elaine

···

On Nov 9, 2014, at 8:17 AM, Anton Feenstra <k.a.feenstra@vu.nl> wrote:

On 08-11-14 23:38, Elaine Meng wrote:

Hi Anton,
Pardon me if I’m duplicating a previous answer, but I didn’t see one…

There are various scores available via the AACon web service connected to Jalview as described here:
<http://www.jalview.org/help/html/webServices/AACon.html>

The Valdar paper cited in that page describes the options in more detail. Some of the scores are SP or very SP-like. I don’t recall seeing sub-options in the AACon dialog, so for some of these it may not be obvious which substituation matrix is used. The Valdar paper is here:
<http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/full>

Since I’m a Chimera person, I’ll also plug that program (very briefly, I know this is the JalView list!). Chimera can calculate sum-of-pairs conservation via the embedded AL2CO method, and you have your choice of a dozen or so different substitution matrices and what proportion of gaps are tolerated in a column. It can’t handle as large alignments as JalView can, however. The conservation values are easily/automatically mapped to any structures associated with the alignment. Tutorial example:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1>

Thanks, I'll look into that!

Jim, I basically need some scoring to compare alignments produced by
different tools/settings. Preferably, I'd use several scores so as not
to be dependent on one. Initially, it is just for students in a
practical, (starting tomorrow), but it is also a recurring use case for
my own research. Directing them to a webserver or even the jalview
console would work fine for this purpose.

Pretty as JalView is, sometimes you just don't want to visually compare
all alternative alignments you may have for a particular dataset ;-O

Thanks for all the helpful info Elaine ! As you pointed out - Jalview's quality score is essentially a sum of pairs calculation for each column based on Blosum62 and normalised for gapped positions. I've been meaning to add in a summary score for the annotation row - but until then, Anton, your students could use the groovy script below:

// Open the Tools->Groovy Console
// paste the following lines in and
// press 'CTRL+R' or 'CMD+R' to execute
// output is sum of quality scores for each alignment

def alf = Jalview.getAlignframes();
print "Title\tQuality sum\n"
def qual;
for (ala in alf)
{
     // ala is an jalview.gui.AlignFrame object
     print ala.getTitle()+"\t";
     // get the conservation object and sum the quality scores
     def alcons = ala.viewport.getAlignmentQualityAnnot();
     qual=0;
     for (q in alcons.annotations)
     {
         if (q!=null) { qual+=q.value; }
     }
     print "\t"+qual+"\n";
}
// end of groovy script

ps. for help with groovy - see here: http://www.jalview.org/help/html/features/groovy.html