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Nucleolar localization sequence Detector (NoD) (version 0.0.1)

What it does

This calls the command line version of the NoD tool from the Barton Group for prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an artificial neural network trained on a set of human NoLSs.

The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded as a special nuclear localization sequence (NLS).

The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein):

  • Sequence identifier
  • Start of NoLS
  • End of NoLS
  • NoLS sequence

If a sequence has no predicted NoLS, then there is no line in the output file for it.

References

M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton. Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Research 38(21), 7388-7399, 2010. http://dx.doi.org/10.1093/nar/gkq653

M. S. Scott, P. V. Troshin and G. J. Barton. NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics, in press, 2011.

http://www.compbio.dundee.ac.uk/www-nod/