PredictNLS

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Contents

Intro

PredictNLS is an automated tool for the analysis and determination of Nuclear Localization Signals (NLS).

You submit a protein sequence or a potential NLS. PredictNLS predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given. If no NLS is found, you can predict the subcellular localization of the protein using LOCtree.

Availability, Downloading and Installing PredictNLS

Server

PredictNLS is available through the PredictProtein server.

Software Download

Please consult the package overview page on how to get PredictNLS. Also check out this Installation Guide.

Running PredictNLS

Please see the PredictNLS man page:

 man predictnls

Help

Input options for PredictNLS Protein Sequence mode: Only one letter symbols for amino acid recidues allowed. Any number of white spaces allowed. NLS discovery mode: Amino acid residues input as one-letter symbol. No white spaces or newline characters allowed. An x (or X) will be matched to any amino acid residue.

Example Motifs
Example 	Read 	Equivalent Motifs
[KR]KRKK 	"K or R" KRKK 	KKRKK,RKRKK
K{5} 	5 times K 	KKKKK
[KR]{3,5} 	between 3 and 5 times K or R 	KKRR, RRKKR, RRR,KKK ...
K{3,}? 	3 or more K's 	KKK,KKKK,KKKKK ...

Interpretation of results:

No NLS found:

This does not imply there is no NLS in your protein, we just don't know it. Thus if you find and verify it, you will have a strong publication. In that case, please send us the NLS you found. This helps us keep the database up-to-date. The submitted protein sequence does not contain any NLS in our database.

Accuracy of NLS reported:

If the reported motif can be traced to an ExperimentalNLS the experimental NLS will be reported. If the reported NLS cannot be traced to any experimental NLS the prediction accuracy can be assessed by the number of nuclear proteins in which this motif is found. All motifs in our NLS database are found in 3 or more families. For more information on the NLS database refer to paper. All NLS's found in the query sequence are highlighted in red in the output report.

Symbols used in representing the NLS are explained below:

An x (or X) implies any amino acid residue can be present at this position.

Example Motifs

Example 	Read 	Equivalent Motifs
[KR]KRKK 	"K or R" KRKK 	KKRKK,RKRKK
K{5} 	5 times K 	KKKKK
[KR]{3,5} 	between 3 and 5 times K or R 	KKRR, RRKKR, RRR,KKK ...
K{3,}? 	3 or more K's 	KKK,KKKK,KKKKK ...

Accuracy of DNA binding prediction: The 'DNA binding NLS' used to predict DNA binding is reported. The prediction accuracy is estimated from the fraction of proteins which bind DNA. The probablility of the NLS being found within the DNA binding domain is estimated.

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