Hi Ahmad - just to add to Mungo here. On 27/05/2019 12:04, Mungo Carstairs (Staff) wrote: > 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 > 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> > > *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.carsta...@dundee.ac.uk <mailto:g.m.carsta...@dundee.ac.uk> > > University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of > Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn > <http://uod.ac.uk/sig-li> University of Dundee YouTube > <http://uod.ac.uk/sig-yt> University of Dundee Instagram > <http://uod.ac.uk/sig-ig> University of Dundee Snapchat > <http://uod.ac.uk/sig-sc> > *We're Scottish University of the Year again!* > <http://uod.ac.uk/sig-strapline> > The Times / Sunday Times Good University Guide 2016 and 2017 > > ------------------------------------------------------------------------ > *From:* jalview-discuss-boun...@jalview.org > <jalview-discuss-boun...@jalview.org> on behalf of Ahmad Khalifa > <underoath...@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 > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss > -- ------------------------------------------------------------------- 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 The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
