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Forming Web-links for protein files and alignments

Strap can be used as an interactive sequence alignment and 3D-viewer and supports sequence position highlighting and annotation and 3D-superposition. It can be used to present information of research projects, to report computed results of web services, in WIKI systems and for online publications. Further, alignment views can be included in E-mails to communicate alignments and important sequence positions.

The following example of a web link loads and aligns three proteins from Uniprot and underlines sequence features:

Advantages of dynamic Java based views over static documents:

Protein files and sequence features are freshly downloaded from public servers, and are therefore up to date.
Protein files can be conveniently transported with the mouse to other applications or locations via Drag and Drop.
The data is completely encoded in the web address, no attachment or additional files are required.
Reduced download due to local cache.

Requirements: Java is needed on the client PC. There are no particular requirements for the Web-server, as the links are static.

Limitations:

For large alignment data, the length of web address may exceed a maximum. Solution: Script commands and HTML forms
Occasionally, Java programs do not start for various reasons.
Rarely, certain Web services such as the EBI services or the PDB-RCSB site are temporarily not available and depending program functions of Strap will not function.

Building the Web-address for launching the alignment view: The information to display the alignment is stored in a web address. STRAP assists the generation of such Web link. The respective dialog is found in "Export alignment" in the menu "File". For most users, it is sufficient to know that the web variable "load" or "align" gives a space separated list of database references such as PFAM:PF00076 or PDB:1sbc or UNIPROT:hslv_ecoli. The space is encoded by a plus sign and the colon ":" by %3A. Details are explained in Web links for Strap.