PSI-BLAST

1
Using Hybrid Algorithm for Iterative Sequence
Database Searches Yuheng Li, Mario Lauria, Ralf
Bundschuh The Ohio State University, Columbus OH

• Position-Specific Gap Cost (PSGC) could enhance
  PSI-BLAST performance

PSI-BLAST

• Smith-Waterman (S-W) algorithm cannot deal with
  PSGC

?

• Hybrid algorithm is an alternative to S-W
  algorithm

position specific gap cost
and it can handle PSGC

• Question
• Does Hybrid fit into PSI-BLAST ?
• (given that PSI-BLAST has been tuned around
  Smith-Waterman)

2
Using Hybrid Algorithm for Iterative Sequence
Database Searches Yuheng Li, Mario Lauria, Ralf
Bundschuh The Ohio State University, Columbus OH

• Question Does Hybrid fit into PSI-BLAST ?

• Answer The current Hybrid prototype (non-PSGC)
  works comparably to Smith-Waterman

• Future Work