iTAK 1.5 – Plant Transcription Factor & Protein Kinase Identifier and Classifier

iTAK 1.5

:: DESCRIPTION

iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).

::DEVELOPER

Fei Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl
  • Bioperl

:: DOWNLOAD

 iTAK

:: MORE INFORMATION

Kinome-render 1.3 – Visualize the Protein Kinase Superfamily of Protein

Kinome-render 1.3

:: DESCRIPTION

Kinome-render is a tool to help visualize the protein kinase superfamily of proteins by overlapping annotation on a template of the phylogenetic tree

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows / MacOsX
  • Perl

:: DOWNLOAD

  Kinome-render

:: MORE INFORMATION

Citation

PeerJ. 2013 Aug 8;1:e126. doi: 10.7717/peerj.126. Print 2013.
Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree.
Chartier M, Chénard T, Barker J, Najmanovich R.

Kinannote 1.0 – Protein Kinase Identification and Classification

Kinannote 1.0

:: DESCRIPTION

Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes.

::DEVELOPER

Kinannote team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • hmmer 2
  • Blast 2.24

:: DOWNLOAD

  Kinannote

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 1;29(19):2387-94. doi: 10.1093/bioinformatics/btt419. Epub 2013 Jul 31.
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
Goldberg JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, Zeng Q.

PKIS – Protein Kinase Identification Server

PKIS

:: DESCRIPTION

PKIS is a novel protein kinase identification web server which presented for the identification of the protein kinases responsible for experimentally verified P-sites at high specificity, which incorporates the composition of monomer spectrum (CMS) encoding strategy and support vector machines (SVMs).

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 13;14:247. doi: 10.1186/1471-2105-14-247.
PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites.
Zou L, Wang M, Shen Y, Liao J, Li A, Wang M.