alignment editor that displays secondary structure

[tevang]

Hi everyone,

I'm strangling to modify a multiple sequence alignment to eliminate disruption of secondary structure elements in the target sequence. For this purpose I generate an image of the MSA with the secondary structure elements placed above the sequence with ESPript server, and then modify the MSA in Jalview, resubmit it to ESPript and so on. As you can understand this procedure is tedious hence I'm seeking a commercial free alignment editor that can display the secondary structure of every template in the alignment (as ESPript does) while the user can modify any of the sequences. I know Maestro from Schrodinger has an alignment editor that can also predict the secondary structure of the target sequence and displays all the secondary structures nicely while the user can modify the alignment interactively. But the problem with Maestro is that it needs a license.

Hope someone can help me with this.

best,
Tom

[ksteczk]

Hi Tom,
Didn't you consider presenting SSE's as additional sequences (e.g. ------HHHHH---HHHH----EEEEE---EEEE---HHH) and concatenate it with the alignment - you'd be able to display it in SEAVIEW and move simultaneously with respective sequences... Of course you'd have to assign positions of SSE's to respective columns in the alignment.
Kamil

[tevang]

Hi Kamil,

yes that would be possible, but as you pointed out I'll have to modify the SSEs accordingly every time I change something in the alignment. Can this be automated with SEAVIEW, is that what you said?

Tom

[ksteczk]

Tom,
You can work on alignment file, which is in fact text file. If you'd like to modify it you may be interested in some text scripting.
You cam also modify alignment in seaview as it allows for sequence edition. I don't know what automation you are thinking about. As I understood you'd like to optimize the alignment to prevent secondary structure disruption. So you need to have secondary structure visualized in real time. But that is what you get with seaview - you have both - MSA block and respective SSEs block displayed simultaneously and you can move them both to adjust the alignment.
But if you need to recompute SSE every alignment alteration, my method wouldn't be efficient to do so. Seaview only visualizes sequences. Do not perform any additional computations on them. I'd rather suggest not to compute SSE basing on adjusted alignment but rather on SSEs profile comprising predictions for every sequence in the alignment (you do not need to recompute SSE but just observe how profile behaves).
Best,
Kamil