Dear developers,
may I request to add an option that can display the secondary structure elements (SSEs) of every sequence with known structure below (or above) the alignment? In conjunction with secondary structure prediction by Jpred, the user could adjust the alignment to eliminate disruption of SSEs in the unknown sequences. With this feature Jalview could become the ultimate commercial free alignment editor for comparative modeling.
best regards,
Thomas
Hi Thomas - thanks very much for this feature request (and the kind words). I've added it to our issue tracker here: http://issues.jalview.org/browse/JAL-674
In principle, its possible to retrieve secondary structure annotation via DAS - there's a server that will return annotation for every PDB code. There are a couple of points where the information flow needs to be joined up in order to get this to happen automatically for any sequence (e.g. retrieve secondary structure for any uniprot sequence with PDB cross references). Watch the comments on this feature request for workarounds and updates.
Jim.
On 06/10/2010 12:15, Thomas Evangelidis wrote:
Dear developers,
may I request to add an option that can display the secondary
structure elements (SSEs) of every sequence with known structure below
(or above) the alignment? In conjunction with secondary structure
prediction by Jpred, the user could adjust the alignment to eliminate
disruption of SSEs in the unknown sequences. With this feature Jalview
could become the ultimate commercial free alignment editor for
comparative modeling.best regards,
Thomas_______________________________________________
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