get all residue positions for a particular column

Jalview Discussion
1

Hi All,
I was wondering if there is a way to get all the residue positions for a particular selected column in an alignment

for eg.

I have 83 sequences in an alignment, I select a particular column , by clikcing on top ,and get the red bar. After this I can mouse over each sequence and see the residue numbers in the bottom.

Is there a way to bulk - output all the residue numbers at a particular column position?

So the output would look like

gi 12134567 833, P
gi 23456789 782 P
gi 12456789 830 P
gi 32737237 - -

…and so on for all 83 sequences more sequences

Thanks for your help
Hari

2

Hello Hari - great to hear from you :slight_smile:

I was wondering if there is a way to get all the residue positions for a particular selected column in an alignment

There isn't a way to get the positions exactly as you want. You could manually get positions by selecting just one column and exporting the region to an alignment file (right click and follow the selection submenu), but that's pretty cumbersome if you need to do it for more than a couple of columns.

I've asked our new Jalview developer, Mungo Carstairs, to take a look at this, since it should be fairly straightforward to put together a groovy script to do what you want.

I have 83 sequences in an alignment, I select a particular column , by clikcing on top ,and get the red bar. After this I can mouse over each sequence and see the residue numbers in the bottom.
So the output would look like

gi 12134567 833, P
gi 23456789 782 P
gi 12456789 830 P
gi 32737237 - -

....and so on for all 83 sequences more sequences

I created a JIRA issue so we can discuss the fine details (http://issues.jalview.org/browse/JAL-1542). For the moment, we were wondering if you wanted to export the positions for a number of columns ?

e.g. for a range of columns highlighted with red column marks output:
# Alignment column 1
gi 12134567 833 P
gi 23456789 782 P
gi 12456789 830 P
gi 32737237 - -
# Alignment column 5
..

Is that the kind of thing you'd need ?

Jim.

···

On 12/09/2014 03:14, hari jayaram wrote:

3

Hi Jim…
Great to be back on jalview discuss. Am looking at a lot of alignments these days and loving the new features in Jalview ( esp the super easy map to structure , secondary structure predicition etc)

Thanks for speedy reply. I was able to get the column residue positions …by a two step process following your hint

  1. Creating a feature by selecting the columns containing the start and stop boundaries–Selection(rigthclick )- Create sequence feature
  2. Then …going to File in main menu and outputting the feature to a file.
  3. That file then contains a csv of feature name and start and stop boundaries

I have another question about Selection output to a FASTA file. In earlier versions the selection would have the start and stop residues of the selection annotated in the fasta file…and not start and stop of the whole sequence: any ideas how to get the old style output. Since this is a separate issue I will ask a separate question here…

Thanks again
Hari

···

On Fri, Sep 12, 2014 at 6:03 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hello Hari - great to hear from you :slight_smile:
On 12/09/2014 03:14, hari jayaram wrote:

I was wondering if there is a way to get all the residue positions for
a particular selected column in an alignment

There isn’t a way to get the positions exactly as you want. You could
manually get positions by selecting just one column and exporting the
region to an alignment file (right click and follow the selection
submenu), but that’s pretty cumbersome if you need to do it for more
than a couple of columns.

I’ve asked our new Jalview developer, Mungo Carstairs, to take a look at
this, since it should be fairly straightforward to put together a groovy
script to do what you want.

I have 83 sequences in an alignment, I select a particular column , by
clikcing on top ,and get the red bar. After this I can mouse over each
sequence and see the residue numbers in the bottom.
So the output would look like

gi 12134567 833, P
gi 23456789 782 P
gi 12456789 830 P
gi 32737237 - -

…and so on for all 83 sequences more sequences

I created a JIRA issue so we can discuss the fine details
(http://issues.jalview.org/browse/JAL-1542). For the moment, we were
wondering if you wanted to export the positions for a number of columns ?

e.g. for a range of columns highlighted with red column marks output:

Alignment column 1

gi 12134567 833 P
gi 23456789 782 P
gi 12456789 830 P
gi 32737237 - -

Alignment column 5

…

Is that the kind of thing you’d need ?

Jim.

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