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At the 23. of december 2008 the first offical release of BLASTScanner has been released. BLASTScanner is a small platform independent console application which translates BLAST-output of the NCBI-BLAST-tool into database code. No installation is required. Just download unpack and run. A single C-Source file is compiled into a very fast and very small application (~30kb). For instance a 20MB-BLAST-file can be translated in 2 seconds into database code suitable being piped into SQLite, MySQL or PostgreSQL-databases. You can download binaries for Win32, Linux32 and Linux64, Mac-OSX, OSF1 and Solaris as well as the C-code for compilation for your platform all together in a 79kb-Zip-file from the sourceforge project page: http://sourceforge.net/projects/bioscanners/
There is the gplex scanner generator (http://plas.fit.qut.edu.au/gplex/) for the C#-programming language. Due to the mono runtime environment (http://www.mono-project.com/) C# code can be run on Win32, Linux and Mac-OSX platforms. As our wc sample run below suggests gplex scanner generated code is slower than Java JIT-compiled code but faster than Java-interpreted code. The mono application requires much less memory.
| Tool/Queries | 1 | 10 | 100 | 1000 | 10000 |
|---|---|---|---|---|---|
| wc-flex | 0.005 | 0.011 | 0.087 | 0.912 | 10.426 |
| wc-java | 0.197 | 0.248 | 0.367 | 1.549 | 14.707 |
| wc-java016 | 0.216 | 0.263 | 0.346 | 1.533 | 14.806 |
| wc-java064 | 0.209 | 0.243 | 0.364 | 1.522 | 14.649 |
| wc-java512 | 0.216 | 0.247 | 0.351 | 1.542 | 16.486 |
| wc-javaip | 0.193 | 0.422 | 2.808 | 28.353 | 331.753 |
| wc-mono1.2 | 0.168 | 0.282 | 1.580 | 15.650 | 175.863 |
| wc-mono2.0 | 0.147 | 0.267 | 1.676 | 15.870 | 187.633 |
| wc-mono2.0-static | 0.150 | 0.272 | 1.670 | 16.265 | 189.411 |
| wc-re2c | 0.004 | 0.006 | 0.038 | 0.382 | 4.301 |
| wc-unix | 0.010 | 0.044 | 0.453 | 4.782 | 54.704 |
wc-mono-static means that a executable with the mono-runtime linked in was tested. Mono-frameworks were 1.2 and 2.0.1. Different options for java memory were tested. java016 means that java was run with the -Xmx16m option.
