Finding alignment and moving it to the top of the list

Jalview Discussion
1

I have 500+ alignments, I tried select find and searched for ID, some residue segments and couldn’t find my sequence of interest! I had to scan the entire list by eye to find it, but then there is the problem of moving it to the top, is there any other way to do it besides clicking ctrl and up for 5 minutes?!

This is the sequence as it appears in the alignment file for reference:

···

XP_001023006.1 tubulin [Tetrahymena thermophila SB210]

------------MREIVHIQGGQCGNQIGAKFWEVISDEHGIDP-----TGTYHGDSDLQ
LERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQTGAGNNWAK
GHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRI
METFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPT–
YGDLNHLVSAAMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQY
RALTVPELTQQMFDAKNMMCAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYF
VEWIPNNIKSSICDIPPKGLKMAVTFVGNSTAI–QEMFKRVAEQFTAMFRRKAFLHWYT
GEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEEGEN----------------

Regards.

2

Hello Ahmad,

Do you have 500+ alignments, or an alignment with 500+ sequences?

Select | Find should highlight the next match of your search pattern in the alignment which has focus. You may have fallen foul of a bug whereby Find matched results in hidden regions. This is fixed in the next release of Jalview (2.11), due out any day now. If this wasn’t your problem, please let us know more details if possible.

Moving a sequence to top: you are right, there is no direct way to do this in Jalview, and we could consider adding one. As a workaround you could:

  1. Edit | Cut and Edit | Paste the sequence to a new alignment window

  2. Select all (remaining) sequences, Copy, and Paste in the new window

This would leave the target sequence at the top (and will be quicker than clicking ‘Up’ arrow a few hundred times!).

Best regards,

Mungo

···

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Ahmad Khalifa underoath006@gmail.com
Sent: 27 May 2019 11:07:11
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Finding alignment and moving it to the top of the list

I have 500+ alignments, I tried select find and searched for ID, some residue segments and couldn’t find my sequence of interest! I had to scan the entire list by eye to find it, but then there is the problem of moving it to the top, is there any other way to do it besides clicking ctrl and up for 5 minutes?!

This is the sequence as it appears in the alignment file for reference:

XP_001023006.1 tubulin [Tetrahymena thermophila SB210]

------------MREIVHIQGGQCGNQIGAKFWEVISDEHGIDP-----TGTYHGDSDLQ
LERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQTGAGNNWAK
GHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRI
METFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPT–
YGDLNHLVSAAMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQY
RALTVPELTQQMFDAKNMMCAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYF
VEWIPNNIKSSICDIPPKGLKMAVTFVGNSTAI–QEMFKRVAEQFTAMFRRKAFLHWYT
GEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEEGEN----------------

Regards.

The University of Dundee is a registered Scottish Charity, No: SC015096

3

Hi Ahmad - just to add to Mungo here.

Select | Find should highlight the next match of your search pattern in
the alignment which has focus. You may have fallen foul of a bug whereby
Find matched results in hidden regions. This is fixed in the next
release of Jalview (2.11), due out any day now. If this wasn't your
problem, please let us know more details if possible.

One thing to remember: The 'Find' dialog searches the alignment that has
current input focus. Remember to click on the title bar of the alignment
that you want to search before hitting the 'Find' button.

Moving a sequence to top: you are right, there is no direct way to do
this in Jalview, and we could consider adding one.

Actually there is an almost direct way to do this (it's one of the quiz
questions in Jalview training courses..):
1. Select the sequence(s) that you want to move to the top or bottom.
2. Press CTRL or CMD + I - this inverts the sequence selection.
3. Press the up or down arrown to move the other sequences up or down
with respect to the sequences you selected in 1.

There are also other ways. For instance if you want to sort according to
the distribution of a particular sequence motif, then use the 'Find All'
option followed by the 'Create Features' to create sequence features for
each hit, then right click on the appropriate feature type (e.g. 'Search
Results' - the default feature name for search results) in the Feature
Settings dialog in order to sort sequences acording to the number of
hits from your search. See Section 4.2.3 of the Jalview Tutorial
(http://www.jalview.org/tutorial/TheJalviewTutorial_v1.9.2.pdf).

As a workaround you

···

On 27/05/2019 12:04, Mungo Carstairs (Staff) wrote:

could:

1) Edit | Cut and Edit | Paste the sequence to a new alignment window

2) Select all (remaining) sequences, Copy, and Paste in the new window

This would leave the target sequence at the top (and will be quicker
than clicking 'Up' arrow a few hundred times!).

Best regards,

Mungo

Email signature

University of Dundee shield logo <http://uod.ac.uk/sig-home&gt;

*Mungo Carstairs*
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

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------------------------------------------------------------------------
*From:* jalview-discuss-bounces@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of Ahmad Khalifa
<underoath006@gmail.com>
*Sent:* 27 May 2019 11:07:11
*To:* jalview-discuss@jalview.org
*Subject:* [Jalview-discuss] Finding alignment and moving it to the top
of the list

I have 500+ alignments, I tried select find and searched for ID, some
residue segments and couldn't find my sequence of interest! I had to
scan the entire list by eye to find it, but then there is the problem of
moving it to the top, is there any other way to do it besides clicking
ctrl and up for 5 minutes?!

This is the sequence as it appears in the alignment file for reference:

XP_001023006.1 tubulin [Tetrahymena thermophila SB210]

------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------MREIVHIQGGQCGNQIGAKFWEVISDEHGIDP-----TGTYHGDSDLQ
LERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLFRPDNFVFGQTGAGNNWAK
GHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYPDRI
METFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPT--
YGDLNHLVSAAMSGVTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQY
RALTVPELTQQMFDAKNMMCAADPRHGRYLTASALFRGRMSTKEVDEQMLNVQNKNSSYF
VEWIPNNIKSSICDIPPKGLKMAVTFVGNSTAI--QEMFKRVAEQFTAMFRRKAFLHWYT
GEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEEGEN----------------
------------------------------------------------------------
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Regards.

The University of Dundee is a registered Scottish Charity, No: SC015096

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The University of Dundee is a registered Scottish Charity, No: SC015096