I was looking for a set of proteins whether they can import into mitochondria by looking at its sequence, using Mitoprot, TargetP and PredSL it was confirmed that these proteins didn't had N-terminal presequence, but there are studies showing Co-localization of these proteins in mitochondria using IF. If these proteins had internal signal sequence rather than N-terminal what would be he best tool to assess them.
Dear Ravi Babu,
you have already used the correct tool to predict the mitochondrial leader sequence (Mitoprot, TargetP and PredSL). As you said, it be possible that your proteins have an internal mitochondrial targeting sequence; but are you sure that these tools aren't able to detect it? in other words, if you take a sort of positive control ( a protein well studied, and in which it was demonstrate the internal target sequence) and you test it with Mitoprot, targetP.... will it be predicted as mitochondrial or not. If the software identifies them as mitochondrial, they work even with non canonical n-term sequence, while if they will not work you can stop to use them and believe to IF ( that however, several time give fake results).
I hope that my answer can be partially useful for you;
regards.
Francesco
As per software webpage it says that these can predict mitochondrial import based on N-terminal sequence but i'm not sure whether it can predict internal sequence unless as francesco said i had a control protein where it has internal sequence but not N-terminal and can import into mitochondria. It would be helpful if you can share your idea if you know any of such control protein.
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