Evaluation of methods for the prediction of membrane spanning regions

By Steffen Möller, M. Croning, Rolf Apweiler. Bioinform., 2001

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ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins1 (2003, methodology): “…polypeptide sequence, and it is not possible to know which prediction program will generate the most accurate prediction for a particular protein (Mo¨ller et al., 2001; Ikeda et al., 2002) Here, we present a novel membrane protein DB, ARAMEMNON, which integrates features that are presently only…”
A combined transmembrane topology and signal peptide prediction method. (2004, background): “Studies have been published on comparisons between different TM prediction methods.(3,33,34) Such comparisons generally turn out to be quite dependent on the test set used; in particular they are sensitive to fraction of proteins having an SP.”
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities (2020, methodology): “0c (27) and Bidirectional Best Hits (BBH) between newly loaded proteomes and IMG reference proteomes are computed using LAST (24).”
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes (2018, methodology): “Next, protein-coding genes undergo prediction of signal peptides and transmembrane regions using SignalP (10) and TMHMM (11), respectively, followed by protein family assignments and functional annotation steps.”
Locating proteins in the cell using TargetP, SignalP and related tools (2007, background): “0 to be the best performing program out of 14 (see ref”