Proceeding talk – Theme: Systems.
Abstract
We present SWORD (Smith-Waterman on reduced database), an efficient protein database search implementation that runs 6-13 times faster than BLASTP in the sensitive mode and up to 44 times faster in the fast and less accurate mode. It is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLASTP for majority of input datasets and provides guaranteed optimal alignments.
Authors
Robert Vaser, University of Zagreb, Faculty of Electrical Engeneering and Computing, Croatia
Dario Pavlović, University of Zagreb, Faculty of Electrical Engeneering and Computing, Croatia
Mile Šikić, University of Zagreb, Faculty of Electrical Engeneering and Computing, Croatia