I am trying to find some tool or server which put secondary structure elements on top of the sequence alignment which ESPRIPT does very well. But is there any other tool which I can use to show the element in 3D view or better than the ESPRIPT visualization. It should use the available PDB to put the elements but not on the basis of prediction. Please suggest if any is there. Thank you, in advance.
look for ExPaSy weblink:
http://www.expasy.org/resources
Depend on your requirement u can select the secondary structure tools.
Dear prem,
you can easily add secondary structure information in multiple sequence alignment by using PRALINE program. In this program u need to input number of sequences is in standard FASTA format.
plz follow the link
http://www.ibi.vu.nl/programs/pralinewww/
the result may be displayed in browser or result may be send to your mailbox depending upon size of input sequences.
the output of PRALINE primarily shows color coded amino acid conservation. then u click on Sec.Structure Button. It display color coded secondary structure information in multiple sequence alignment. save it into PDF.
You can use PSIPRED and SOPMA tools for your work, it may useful as per your i think.
You can also try ESPript 3.0. Use the server in below given link.
All the Best.
http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi
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