Signalp Versus Targetp - Different Scores For Secretory Pathway

Question

[Scg_Bio]

Hi, I'm using signalp and targetp for subcellular localization. targetp presumably calls signalp for its secretory pathway prediction.

"TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).

For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted."

However when I run both programs, signalp and targetp, for one sequence e.g.

1) ENSP00000386201,TAS2R41 taste receptor type 2 member 42

score for targetp=0.987 secretory=YES, and signalp=0.366, secretory=NO.

2) another example: calcium sensing receptor:(NP_000379.2)

here both programs predict secretory pathway but targetp score=0.928 and signalp score= 0.847.

I get different scores for secretory pathway localization. While this doesn't matter in some cases since the prediction gives the same outcome, it matters for others very much, and for the same input dataset of 6000 proteins I get about 600 sequences for secretory pathway for each program but only about 400 of them overlap.

Does anyone know what is happening differently in these 2 programs and what program you would recommend for secretory pathway prediction?

Answer 1

[Lars Juhl Jensen]

TargetP 1.1 uses SignalP 3.0 for the secretory predictions, whereas the SignalP web site runs SignalP 4.0 - that explains the difference you see. I would recommend using SignalP 4.0 for prediction of secreted proteins.

Given what has been changed between version 3.0 and 4.0 of SignalP, I would expect that you mainly see differences for transmembrane proteins.

Answer 2

[Scg_Bio]

Thanks Lars! that helps a lot!

[Lars Juhl Jensen]

You are very welcome - and welcome to BioStar. For the future please post such comments as a "comment" on the reply and not as a "reply" to the question :-)