Expedited batch processing and analysis of transposon insertions

BMC Research Notes

Table 1 Benchmarks

	Size (Mb)	Sequence Number	Hits Extracted	Extraction Time (s)
Anolis carolinensis (AnoCar2.0)	1817	7233	68820	68
Arabidopsis thaliana ( TAIR9.171)	97	1447	9506	4
Aspergillus nidulan (FGSC A4 s06-m03-r02)	31	248	459	1
Homo sapiens (GRCh37)	3147	47650	254941	118
Loxodonta africana (loxAfr3)	3785	233134	52874	135
Macropus eugenii (Meug_1.1)	3013	616418	24627	145
Oryctolagus cuniculus (OryCun2.0)	3537	215471	53097	121
Petromyzon marinus (petMar1)	1049	108241	11086	35
Zea mays (B73 RefGen v2)	2095	31719	246699	100

All benchmarks were performed on a Dell PrecisionT3500 with Intel Xeon E5530 2.40 GHz processor and 6 GB of RAM running Windows XP 64. Example organisms are listed in the first column with the genome version listed in parenthesis. The Size column lists the genome database used in megabytes. The Sequence Number column lists the number of FASTA sequences found in the database file. The Hits Extracted column lists the total number of BLAST hits extracted from the database file. The Extraction Time lists the time in seconds required to extract the Hit Objects from the FASTA-formatted genome database.

ISSN: 1756-0500