Where can I find either a reliable annotation of NLS signals in proteins for various genomes (e.g. for UniProt IDs), or a tool that will take a protein sequence and return an annotation of where NLS's might lie, along their confidence?
I prefer not to use Rost lab NLSPredict since it's commercial / requires license and has a web interface. I want something that can be run in batch mode from the command line, or an annotation that was already applied to the proteome. Thanks.
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Regarding the NLS annotation in UniProtKB:
From the UniProtKB user manual: http://www.uniprot.org/manual/motif Nuclear localization signals are characterized by a high content of basic residues. They are highly degenerate and are annotated only when there is experimental evidence demonstrating their targeting function.
The following link allows you to retrieve all UniProtKB/Swiss-Prot entries with NLS annotations: http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3Amotif+%22nuclear+localization+signal%22%29&sort=score
You can use the above link (or any link in the download page for that query: http://www.uniprot.org/uniprot/?query=annotation%3a%28type%3amotif+%22nuclear+localization+signal%22%29&sort=score&format=* ) programmatically. Have a look at the UniProt FAQ for programmatic access: http://www.uniprot.org/faq/28
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