Transmembrane Topology Prediction Methods: A Re-assessment and
Improvement by a Consensus Method Using a Dataset of
Experimentally-Characterized Transmembrane Topologies
Affiliations: Science of Bioresources Program, The United Graduate
School of Agricultural Sciences, Iwate University, Morioka 020-8550,
Japan | Department of Electronic Information System
Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki
036-8561, Japan
Note: [] *
Abstract: We selected 10 transmembrane (TM) prediction methods (KKD, TMpred,
TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0 and HMMTOP 2.0)
and re-assessed its prediction performance using a reliable dataset with 122
entries of experimentally-characterized TM topologies. Then, we
improved prediction performance by a consensus prediction
method. Prediction performance during re-assessment and consensus
prediction were based on four attributes: (i) the number of transmembrane
segments (TMSs), (ii) the number of TMSs plus TMS-position, (iii) N-tail
location and (iv) TM topology. We noted that hidden Markov
model-based methods dominate over other methods by individual prediction
performance for all four attributes. In addition, all top-performing
methods generally were model-based. Among prokaryotic sequences,
HMMTOP 2.0 solely topped among other methods with prediction accuracies ranging
from 64% to 86% across all attributes. However, among eukaryotic
sequences, prediction performance for all the attributes was relatively poor
compared with prokaryotic ones. On the other hand, our results
showed that our proposed consensus prediction method significantly improved
prediction performance by, at least, an additional nine percentage points
particularly among prokaryotic sequences for the number of TMS (84%), number of
TMS and position (80%), and TM topology attributes (74%). Although
our consensus prediction method improved also the prediction performance among
eukaryotic sequences, the obtained accuracies for all attributes were
relatively lower than that obtained by prokaryotic counterparts particularly
for TM topology.
