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In the homology-based methods, e.g. Pfam (Finn et al., 2010), CHOP (Liu and Rost, 2004) and FIEFDOM (Bondugula et al., 2009), target sequences are searched through known protein structure or family libraries by hidden Markov model (HMM) or PSI-BLAST programs.
Whereas eTBLAST runs on a 40 CPU cluster and typically compares one abstract to all others in PubMed in ∼40 s to 1 min, the SIPs of an abstract are searched through PubMed in 69 s on average and the process can be run on a single CPU.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com