NNAlign 2.1 – Discovering Sequence Motifs in Quantitative Peptide data

NNAlign 2.1

:: DESCRIPTION

NNAlign is a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NNAlign

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e26781. doi: 10.1371/journal.pone.0026781. Epub 2011 Nov 2.
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data.
Andreatta M1, Schafer-Nielsen C, Lund O, Buus S, Nielsen M.

ScanSite 3 – Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover

ScanSite 3

:: DESCRIPTION

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

::DEVELOPER

ScanSite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
Obenauer JC, Cantley LC, Yaffe MB.
Nucleic Acids Res. 2003 Jul 1;31(13):3635-41.

TransModis – Sequence Motif and Gene Expression or ChIP-binding data to Identify TF Binding Sites

TransModis

:: DESCRIPTION

TransModis is a generalization of MODEM to consider sequence motif and multiple gene expression or ChIP-binding experiments to identify TF binding sites.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TransModis

:: MORE INFORMATION

Citation

Yu RX, Liu J, True N, Wang W (2008)
Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16.
PLoS ONE 3(3): e1821. doi:10.1371/journal.pone.0001821