bowtie, tophat vs BLAST

Hi,

I have a very basic question but it confused me a little bit. 

For a metatranscriptome data, we can compare it with the NCBI prokaryote genome collections. Shall I use bowtie, tophat these kinds of mapping tools here, or just use BLAST here? What's the difference between this two kinds of tools? What kind of different downstream analysis would be available only for one tool?

Thanks!