Figure 6
From: Shape based indexing for faster search of RNA family databases
Runtime comparison. Average runtime in seconds vs. sequence length for the four different search methods: "cmsearch": for all R families in the database a cmsearch is executed until a match or all families were searched. "HMM-filter": The same as "cmsearch" but with activated "-hmmfilter" option. The measured time is just the runtime for the real search not for the construction of the HMM. We assume that this could be done once for a fixed Rfam release. "BLAST-filter": the Rfam Perl script "rfam_scan.pl" from the Rfam website is used. "RNAsifter" uses the k-best-shape-index with the suggested parameter set. The considered sequences for this comparison is the whole testset.