Figure 1
From: HMM-ModE: implementation, benchmarking and validation with HMMER3
Benchmarking the HMM-ModE protocol with HMMERv2 and HMMERv3. The protocol was benchmarked with both versions of HMMER v2 – which permits Glocal alignments – and HMMER v3 which only has local-local alignments on a dataset of 416 enzyme families. Specificity values reported during profile building are improved in all cases, with minimal loss in sensitivity. The specificity improvement is lower for HMMER v3 compared to the earlier version.