iHSP-PseRAAAC – Identifying the Heat Shock Protein Families

iHSP-PseRAAAC

:: DESCRIPTION

The web-server iHSP-PseRAAAC was developed to identify the family of heat shock proteins by using reduced amino acid alphabet.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Anal Biochem. 2013 Nov 1;442(1):118-25. doi: 10.1016/j.ab.2013.05.024. Epub 2013 Jun 10.
iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition.
Feng PM1, Chen W, Lin H, Chou KC.

MinPath 1.4 – Biological Pathway Reconstructions using Protein Family Predictions

MinPath 1.4

:: DESCRIPTION

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MinPath

:: MORE INFORMATION

Citation:

Yuzhen Ye and Thomas G. Doak.
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PLoS Computational Biology, 5(8): e1000465 (2009)

CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity

CLANS 20101007

:: DESCRIPTION

CLANS (CLuster ANalysis of Sequences) is a software for visualizing protein families based on pairwise similarity. A clustering is performed based on all against all BLAST similarities and the detected groups are returned. Only BLAST similarities better than a specified cutoff are used to perform the cluster analysis.

::DEVELOPER

CLANS team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CLANS

:: MORE INFORMATION

Citation:

Frickey, T. and Lupas A. N. (2004)
CLANS: a Java application for visualizing protein families based on pairwise similarity.
Bioinformatics, 20(18), 3702-3704.

PDEXK – Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily

PDEXK

:: DESCRIPTION

The PDEXK server is developed for detecting new protein families of the PD-(D/E)XK superfamily using Support Vector Machines trained on data derived from profile-profile alignments. Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Laganeckas M., Margelevičius M., Venclovas Č. (2010)
Identification of new homologs of PD-(D/E)XK nucleases by Support Vector Machines trained on data derived from profile-profile alignments.
Nucl. Acids Res. (2011) 39 (4): 1187-1196.

PFSTATS – Analyze Protein Families using simple Statistics

PFSTATS

:: DESCRIPTION

PFSTATS is a set of programs and scripts devoted to analyze protein families using simple statistics.

::DEVELOPER

the Protein Computational Biology group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX

:: DOWNLOAD

  PFSTATS

:: MORE INFORMATION

MaxSubTree – Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence

MaxSubTree

:: DESCRIPTION

MaxSubTree is a combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 MaxSubTree

:: MORE INFORMATION

Citation

J.Baussand, A.Carbone.
A combinatorial approach to detect coevolved amino-acid networks in protein families with variable divergence,
PLoS Computational Biology 5(9) e1000488 (2009)

SIFTER 2.1.1 – Genome-scale Phylogenetic Function Annotation of Protein Families

SIFTER 2.1.1

:: DESCRIPTION

SIFTER (Statistical Inference of Function Through Evolutionary Relationships) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. SIFTER allows annotations to be made on a genomic scale.

::DEVELOPER

SIFTER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 SIFTER

:: MORE INFORMATION

Citation:

B.E. Engelhardt, M.I. Jordan, J.R. Srouji, and S.E. Brenner (2010).
Genome-scale phylogenetic function annotation of large and diverse protein families
Genome Res. 2011 July 22, 2011, doi:10.1101/gr.104687.109

DIVERGE 2.0 – Detect Functional Divergence between member Genes of a Protein Family

DIVERGE 2.0

:: DESCRIPTION

DIVERGE is designed to detect functional divergence between member genes of a protein family, based on (site-specific) shifted evolutionary rates after gene duplication or speciation. Posterior analysis results in a site-specific profile for predicting important amino acid residues that are responsible for functional divergence. Moreover, when the 3D protein structure is available, these predicted sites can be mapped to the 3D structure viewer to explore its structure basis.

::DEVELOPER

Xun Gu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 DIVERGE

:: MORE INFORMATION

Citation:

Gu, X. (1999)
Statistical methods for testing functional divergence after gene duplication.
Molecular Biology and Evolution 16:1664-1674.

MORPH – Predict Protein Interaction Partners between members of two Protein Families

MORPH

:: DESCRIPTION

MORPH predicts protein interaction partners between members of two protein families that are known to interact (for example: Ligands and Receptors).

::DEVELOPER

Raja Jothi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • perl 

:: DOWNLOAD

 MORPH

:: MORE INFORMATION

Citation

Raja Jothi, Maricel Kann,and Teresa M. Przytycka
Predicting Protein-Protein Interaction by Searching Evolutioinary Tree Automorphism Space.
Bioinformatics. 2005 June; 21(Suppl 1): i241–i250.

Quicktree 1.1 – Reconstruction of Phylogenies for very large Protein Families

Quicktree 1.1

:: DESCRIPTION

QuickTree allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods.

::DEVELOPER

Kevin Howe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 Quicktree

:: MORE INFORMATION

Citation

QuickTree: building huge Neighbour-Joining trees of protein sequences.
Howe K, Bateman A and Durbin R
Bioinformatics 2002;18;11;1546-7