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

PFSTATS 0.98 – Analyze Protein Families using simple Statistics

PFSTATS 0.98

:: 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)

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

:: 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.

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

:: 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

Linux / Windows / Mac OsX
NCBI BLAST
Java

:: 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.

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