The speed of SENCEL PARALIGN
How fast is PARALIGN compared to other software?
In the graph below, the total time used to search with 11 different
database is shown for PARALIGN, Sencel's Smith-Waterman
implementation (SW), BLAST, SSEARCH and FASTA with ktup 1 and
2. The searches were run on a computer with an Intel Xeon 2.8GHz
As can be seen from the graph, PARALIGN is almost as fast as
BLAST, while SW is about eight times slower. SW is still about
six times as fast as SSEARCH, which is a Smith-Waterman implementation
not using multimedia technology. SW is also faster than FASTA with
ktup 1, while FASTA with ktup 2 is in between ParAlign and SW in
How fast is PARALIGN on different computers?
The graph below shows the total time used to search
database with 11 different
using PARALIGN, Sencel's Smith-Waterman
implementation (SW) and BLAST on different computer systems.
As can be seen on the graph, the speed is quite similar across
all of these processors. On the same type
of processor, the
speed scales nearly linearly with
How was this high speed achieved?
The speed of Sencel's software has been achieved using a parallel
processing technology known as multimedia technology or SIMD which
is embedded in most modern microprocessors. Read more about this
technology on the page about multimedia
The speed tests were performed using a
set of query sequences in the range of 143 to 567 amino acids (SWISS-PROT
P00762, P01008, P01111, P02232, P03435, P05013, P07327, P10318,
P10635, P14942 and P25705). These sequences were used as a query
against the SWISS-PROT database release 40 (37 315 215 amino acids
602 entries). The BLOSUM62 score matrix was used in combination
penalty of 11+k, where k is the gap length. Default statistics
and an expect value of 10 was used, a maximum of 100 hits where
and no alignments were computed. Searches were
performed with a single thread, and the time shown is total cpu
user time for all searches. Software used:
PARALIGN version 3.3.7, NCBI
2.2.6, FASTA and SSEARCH version 3.4t23b2. Hardware used:
Dell Precision Workstation with dual Xeon 2.8 GHz processors, Apple
Power Mac G5 with dual PowerPC
G5 2.0GHz processors, HP Superdome with Itanium 2 1.5GHz processors.