SCANPS -- a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
What you can do:
Protein sequence database searching.
Highlights:
- SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance.
- This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks.
- Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases.
- The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains.
- The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly.
- For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.
Keywords:
- iterative profile searching
- PSI-BLAST
- domain searching
- protein sequence databases
- SCOP
- protein sequence
Literature & Tutorials:
This record last updated: 07-16-2008