Fig. 4From: MultiDomainBenchmark: a multi-domain query and subject database suiteAbbreviated command-line examples for non-iterative searches. For BLAST, we searched with PSI-BLAST set to a single iteration on the MultiDomainBenchmark target database. For non-iterative HMMER, we first produced a hidden Markov model (HMM) with hmmbuild, then searched the MDB target database using that HMM with hmmsearch. For PSI-BLAST, first, we search for up to five iterations on a clustered version of the NR database (see main text for details), saving the resulting position-specific scoring matrix (PSSM). Then, using the resulting PSSM, we searched the MDB target database. For iterative HMMER, we saved the resulting HMM produced by searching up to five iterations with jackhmmer. Then, we performed a final search on the MDB target database with hmmsearch using the resulting HMM. The e-value threshold (and -num_descriptions and -num_alignments) were set artificially high for performance analysis reasons. For complete command-line usage, see the MDB websiteBack to article page