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 protein query sequences against the SWISS-PROT 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 processor.

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 speed.

How fast is PARALIGN on different computers?

The graph below shows the total time used to search the SWISS-PROT database with 11 different protein query sequences 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 the CPU clock frequency.

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 technology.

Test conditions

The speed tests were performed using a set of query sequences in the range of 143 to 567 amino acids (SWISS-PROT accession numbers 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 in 101 602 entries). The BLOSUM62 score matrix was used in combination with a gap 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 listed 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 BLAST version 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.