Protein database searching is a common operation in the genome annotation and de novo transcriptome annotation. However, the process always consume huge computing resources. Like the searching of NCBI NR database. Although many protocals have been provided, the application of them is not limited. BLAST still be the widely used program. I am wonder whether there is an alternative? PLAST is such one, which can be deployed easily on the prevalent multi-core desk computer in contrast to those constructed based on the infrastructure, like GPU-blast and FGPA-blast.
My question is why there is few people choose PLAST? Vouzis [1] has pointed that the results of PLAST had 4% difference to BLAST (Table 4 in PLAST paper). I have rechecked that paper, and found that the difference at 1e-3 is ~2%. The difference will be narrow when the e-value decrease.
1 Vouzis, P. D. & Sahinidis, N. V. GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics 27, 182-188 (2011).
Has anyone tried this software?
My question is why there is few people choose PLAST? Vouzis [1] has pointed that the results of PLAST had 4% difference to BLAST (Table 4 in PLAST paper). I have rechecked that paper, and found that the difference at 1e-3 is ~2%. The difference will be narrow when the e-value decrease.
1 Vouzis, P. D. & Sahinidis, N. V. GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics 27, 182-188 (2011).
Has anyone tried this software?