In contrast PSORTII (k-NN prediction) predicts a nuclear protein (43.5% probability) or mitochondrial localization (39.1%).
Prediction schemes predict a certain sample value by a linear or non-linear combination of its spatial neighbours and encode the difference of the sample value and its prediction (prediction error).
On the other hand, similar to PenB_MT2, secondary structure prediction programs predict a complex, conserved secondary structure element pattern built from both α-helices and β-strands.
16 Many existing coiled coil prediction methods predict a continuous coiled coil and also are capable of reporting stutters and stammers.
Three main streams have been identified for comparative RNA secondary structure prediction: (i) predict a structure from a pre-computed sequence alignment; (ii) simultaneously compute an alignment and a structure and (iii) alignment-free methods (Gardner and Giegerich, 2004).
First, we do not know whether thermodynamic mRNA structure predictions predict the mRNA structures that are formed in the cell.
Then, the same could be considered for protein Ssu05_2173, which has been annotated as a LysM protein: PSORTb predicts it to be a cell-wall protein, whereas feature-based methods did not agree in their predictions: SignalP predicted a signal peptide, with a cleavage site in 38 39, and TMHMM predicted a TMH in residues 7 26.
After 110 min, we then simulated a blebbistatin treatment as an exponential decrease in contractility, following previous experimental results on traction force decrease with blebbistatin (Lam et al., 2012; details in Appendix 5: model predictions), which predicted a rapid migration back towards the anterior pole.
An NADH-dependent glutamate synthase (SP−/TP+) was also identified; however, the ChloroP TP prediction program predicted a cTP sequence, whereas other TP prediction programs (IPSort; PredSL) indicated an mTP.
As shown in Section 3.4, the proposed prediction method can predict a pixel with its four immediate pixels, and all the pixels can be predicted completely with original pixels as context.
