Percent identity between 2 rows

Jalview Discussion
1

I want to calculate the percent identity between 2 sequences in an alignment. Selecting Pairwise identity doesn’t use the alignment from the main window but calculates its own (i.e. not with the same gaps). Suggestions? Can one derive the %identity from the score or distance?

Also, how can one use the "select column by annotation" to select only those columns with conservation = 11 ? It doesn’t seem to work for me.

Thanks,
Mark

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_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III saper@umich.edu +1 (734) 764-3353

2

Hello Mark

I want to calculate the percent identity between 2 sequences in an alignment. Selecting Pairwise identity doesn’t use the alignment from the main window but calculates its own (i.e. not with the same gaps).

You mean 'Pairwise alignment' I think here - yes - that's currently the
only way Jalview easily produces a PID report.

Suggestions? Can one derive the %identity from the score or distance?

yes - of course :slight_smile: The introduction of the calculation dialog box was
the first step towards allowing PID matrices to be exported from
Jalview, but we haven't quite finished that functionality yet. We'll
post a groovy script tomorrow that should do what you want.

Also, how can one use the "select column by annotation" to select only those columns with conservation = 11 ? It doesn’t seem to work for me.

Thanks for pointing that out - right now, you have to enter '*' in the
label box to select those columns. We'll take a look at what's going on
for the next release...

Jim.

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On 19/10/2017 17:23, Mark Saper wrote:

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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

3

Hi again, Mark.

…Jalview, but we haven’t quite finished that functionality yet. We’ll post a groovy script tomorrow that should do what you want.

You can download a script here:
http://www.jalview.org/builds/release/examples/groovy/PIDmatrix.groovy

First open Jalview’s groovy console and load the script file, then use the ‘Execute Groovy Script’ from an alignment window’s calculate menu to get a percent identity matrix generated for the visible area of the alignment or the current selection. The matrix is output in ‘relaxed PHYLIP’ format.

This script supports a range of different PID calculations - the different possibilities are described in the comments, which include variants examined in a paper published by GPS Raghava and Geoff:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-415

As I said in the previous email, we’re hoping to make this a little simpler if a future version, but for now, let us know how you get on !

Jim.

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On 19/10/2017 19:27, Jim Procter wrote: