GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

BMC Bioinformatics

Table 1 Running time comparison of GRASPx and PSI-BLAST on DS2

Query	Num.	GRASPx			PSI-BLAST
genome	prot.	CPU	Wall	Perc. CPU	CPU	Wall	Perc. CPU
SGO	2051	148h55m	9h36m	1553 %	29h20m	9h52m	304 %
PAC	2297	157h40m	10h01m	1574 %	26h27m	8h35m	315 %

‘Query genome’ indicates the genome from which the query sequences were obtained; SGO: Streptococcus gordonii; PAC: Propionibacterium acnes. ‘Num. prot.’ indicates the number of protein sequences that are annotated in the corresponding genome and used as the queries. ‘CPU’ and ‘Wall’ indicate the CPU time and wall-clock time for the corresponding program to search all query proteins sequences against DS2, respectively. ‘Perc. CPU’ indicates the percentage of CPU used for the search (both programs were assigned with 16 CPUs; PSI-BLAST only used 4 CPUs at maximum)

ISSN: 1471-2105