BlastParsers vs BlastScanners

We recently compared our newly generated Blast scanners with currently available BLAST-scanners from the BioJava-project [1], the BioPerl-project [2] and with the Zerg-BLAST parser [3]. Those parsers were compared with our scanners created either with C-based scanner generators like Re2c [4] and Flex [5] or with the Java based scanner generator Jflex [6]. Wheras the parsers mentioned above requires source code editing for parsing and analysing blast files our scanners are emitting SQL-code. Analyzing of blast results can afterwards done with a high level language (SQL). Please note that the BioJava scanner does not work with actual BLAST-versions. File sizes for the blast files has been about 1 (small), 14 (medium) and 140 (large) Mb

Mode	small	medium	large	memory(Mb)
blast-biojava	2.019	8.055	err	1054
blast-bioperl	4.026	47.822	nd	21
blast-flex	0.051	0.567	4.237	20
blast-jflex	0.607	1.906	8.532	863
blast-re2c	0.027	0.283	2.094	19.7
blast-zerg	0.017	0.185	1.331	6.5
blast-tclkit851	35.480	nd	nd	10.1