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.
  • 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.
  • iterative profile searching
  • domain searching
  • protein sequence databases
  • SCOP
  • protein sequence
This record last updated: 07-16-2008
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