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Because FastBLAST's merge operates on reduced sets of sequences as ordinary FastBLAST does, it should give a similar speed-up over BLAST and similar accuracy.
Despite this, ETA network diffusion had a consistent 4% accuracy advantage for 3 EC digit annotations over BLAST down to a z-score of 0.3, or 81% coverage (Figure S1B).
Future developments are planned to be able to implement different sources of data, such as the integration of protein domain profile searches and specialized protein databanks annotated with GO, in order to improve the functional coverage and predictive power tested over BLAST and UniProtKB.
This is an advantage in high-throughput environments over BLAST, for instance, since post-processing filtering scripts are not needed.
Therefore, in the naming procedure class specific methods are preferred over BLAST, which in turn is preferred over Infernal/Rfam.
The result of these experiments, which is consistent with [ 62], is that FASTA should be preferred over BLAST for ncRNA searches.
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