You are currently browsing the monthly archive for April 2007.
Sample: BlastFile with 1 to 10.000 result items
| Mode | 1 | 10 | 100 | 1000 | 10000 |
|---|---|---|---|---|---|
| flex | 0.003 | 0.015 | 0.199 | 1.979 | 25.548 |
| flex-tcl | 0.005 | 0.018 | 0.167 | 1.775 | 20.701 |
| gcj | 0.099 | 0.149 | 0.784 | 7.536 | 83.421 |
| gij | 0.109 | 0.482 | 4.917 | 51.939 | nd |
| java | 0.228 | 0.348 | 0.753 | 3.048 | 27.806 |
| javaip | 0.180 | 0.517 | 4.715 | 49.852 | nd |
| plex | 0.011 | 0.082 | 0.856 | 9.565 | 107.987 |
| perl | 0.031 | 0.050 | 0.235 | 2.280 | 23.916 |
| re2c | 0.004 | 0.012 | 0.076 | 0.765 | 8.438 |
| tcl | 1.702 | 12.524 | 140.249 | nd | nd |
The Re2c based scanner is the fastest, but the setup and the coding is more complicated than for the other scanners.
Flex-based scanners are 2-3 times slower than Re2c based scanners, regardless if there is an embedded Tcl-interpreter for better string handling (flex-tcl), Jflex code (java), executed with the Sun-Java Hotspot virtual machine (1.5) as well as to machine code compiled Jflex code (java-gcj) and Plex (sbs-plex = Pascal lex) based scanners are about 5 and 10 times slower than Re2c based scanners. Interpreted Java-Code either executed with the Sun-interpreter (java-ip = “java -Xint”) or with the gnu-interpreter (java-gij) is about 50 times slower than Re2c-Code. The Tcl based scanner is about 1000 times slower than the Re2c based. The per scanner is a line based scanner thereof not able to do complicated scanning with more than two states or patterns on the same line.
Some new documentation about the aim of the bioscanners project is now online.
