LOCALIZER

Output format

LOCALIZER will return the output as shown in the example below. First, a summary table will be shown which shows the predictions (chloroplast, mitochondria or nucleus) for each submitted protein. If a transit peptide is predicted, the start and end positions in the submitted sequences are shown, alongside the probability. In this example, ToxA has a predicted chloroplast transit peptide with probability 0.885 at position 62-130 in its sequence. LOCALIZER does not return a probability for nucleus localization, because it uses a simple NLS search. In this example, LOCALIZER found a NLS in CRN15, i.e. the sequence KRKR.

In the summary statistic, we count LOCALIZER predictions that are 'chloroplast', 'chloroplast and possible mitochondrial', 'chloroplast and nucleus' and 'chloroplast & possible mitochondrial and nucleus' as chloroplast predictions (same strategy for mitochondrial predictions). A protein that carries a predicted transit peptide with an additional predicted NLS might have experimental evidence only for one of those locations due to the technical hurdles of recognizing dual targeting and should thus not necessarily be counted as a false positive prediction. However, in the LOCALIZER paper, a protein was counted as a nucleus prediction only if it has the category 'nucleus' to avoid assigning a protein to multiple predictions in the evaluation and this is what we recommend.

Example output


# -----------------
# LOCALIZER 1.0 Predictions
# -----------------
Identifier	Chloroplast       	Mitochondria      	Nucleus
CRN15     	-                 	-                 	Y (KRKR)
Ecp2      	-                 	-                 	-      
AVR-Pii   	-                 	-                 	-      
ToxA      	Y (0.885 | 62-130)	-                 	-


# Proteins analyzed: 4

# Number of proteins with cTP: 1 (25.0%)
# Number of proteins with cTP & possible mTP: 0 (0.0%)
# Number of proteins with cTP & NLS: 0 (0.0%)
# Number of proteins with cTP & possible mTP & NLS: 0 (0.0%)
# Number of proteins with mTP: 0 (0.0%)
# Number of proteins with mTP & possible cTP: 0 (0.0%)
# Number of proteins with mTP & NLS: 0 (0.0%)
# Number of proteins with mTP & possible cTP & NLS: 0 (0.0%)
# Number of proteins with NLS and no transit peptides: 1 (25.0%)

# Summary statistics

# Number of proteins with chloroplast localization (cTP, cTP & possible mTP, cTP & NLS, cTP & possible mTP & NLS): 1 (25.0%)
# Number of proteins with mitochondrial localization (mTP, mTP & possible cTP, mTP & NLS, mTP & possible cTP & NLS): 0 (0.0%)
# Number of proteins with nuclear localization and no transit peptides: 1 (25.0%)
# Number of proteins with nuclear localization and with transit peptides: 0 (0.0%)