Hello Kate. Apologies for adding yet another response to Mungo's two suggestions.
Your email suggests the 'Position 1' you talk about is position '1' of the alignemnt ruler, which counts columns rather than sequence positions. If one of your sequences is longer than the others, and there are no insertions in the other sequences, then the ruler will indeed reflect the position of that sequence, but Jalview isn't doing anything special here - just showing the column numbers. If you'd like to have the ruler show positions with respect to a particular sequence, however, then right-click on that sequence's ID and select the 'Set As Reference' option from the submenu. Now, the alignment ruler reflects positions with respect to your 'reference' sequence. As Mungo says - if we still haven't worked out what you were asking, then let us know - but please also let us know if this helped you out ! Jim. On 31/08/2020 09:24, Mungo Carstairs (Staff) wrote: > Hello Kate, > > I'm not quite sure what the question is, so I'll answer two ways. > > You can change the order of sequences in the alignment by clicking on > the sequence name and dragging them up or down. > > You can change the start position of a sequence by right-clicking on the > name, and following the popup menu to > <Sequence Name> | Edit Name/Description > and then type the desired /start-end after the sequence name, for example > myproteinname/20-88 > If you don't want to do the math(s) to work out the end position, just > type /20-20 and Jalview will work it out for you. > > Position numbering is per sequence, so changing it to "start on a > different sequence" doesn't make sense, or perhaps I haven't understood > your question properly. > > One more detail: if you want to save your alignment as a Fasta (or other > format) text file, then check/tick the box for "Append /start-end" for > the file format in Jalview Preferences' Output options panel. You'll > find Preferences under the Tools menu. If you don't do this, sequences > will revert to starting at position 1 after saving and reloading. > > I hope that helps, if not please ask again! > > Best, > > MungoEmail 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> > [email protected] <mailto:[email protected]> > > 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:* [email protected] > <[email protected]> on behalf of Kate Kim > <[email protected]> > *Sent:* 31 August 2020 04:06 > *To:* [email protected] <[email protected]> > *Subject:* [Jalview-discuss] How to change numbering on my alignment? > Hello, > > I have an alignment of five sequences. Position 1 starts on one of the > sequences, but I would like to change it to start on a different > sequence. How can I do this? > > Thank you, > Kate > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > _______________________________________________ > Jalview-discuss mailing list > [email protected] > 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 _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
