CPhos 1.0.5 – Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites

CPhos 1.0.5

:: DESCRIPTION

CPhos utilizes an information theory-based algorithm to assess the conservation of phosphorylation sites among species. A conservation established from this approach can be used to potentially assess the functional significance of a particular phosphorylation site.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

CPhos

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

CPhos

:: MORE INFORMATION

Citation

CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites.
Zhao B, Pisitkun T, Hoffert JD, Knepper MA, Saeed F.
Proteomics. 2012 Nov;12(22):3299-303. doi: 10.1002/pmic.201200189.

ppiPre 1.9 – Predict Protein-Protein Interactions Based on Functional and Topological Similarities

ppiPre 1.9

:: DESCRIPTION

ppiPre is an open-source framework for PPI analysis and prediction using a combination of heterogeneous features including three GO-based semantic similarities, one KEGG-based co-pathway similarity and three topology-based similarities.

::DEVELOPER

Yue Deng <anfdeng at 163.com>, Rongjie Shao, Gang Wang and Yuanjun Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 ppiPre

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013;7 Suppl 2:S8. doi: 10.1186/1752-0509-7-S2-S8. Epub 2013 Oct 14.
ppiPre: predicting protein-protein interactions by combining heterogeneous features.
Deng Y, Gao L, Wang B.

M-Finder – Functional Association Pattern Mining

M-Finder

:: DESCRIPTION

M-Finder is an interactive web application to visualize the functional association pattern (i.e., the functional module) of a gene entered by a user.

::DEVELOPER

BIONETWORK LAB, Baylor University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteome Sci. 2013 Nov 7;11(Suppl 1):S3. doi: 10.1186/1477-5956-11-S1-S3. Epub 2013 Nov 7.
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations.
Cho YR, Mina M, Lu Y, Kwon N, Guzzi PH.

RegRNA 2.0 – an integrated web server for Identifying Functional RNA Motifs and Sites

RegRNA 2.0

:: DESCRIPTION

RegRNA is an integrated web server to comprehensively identify homologs of functional RNA motifs and sites in an RNA sequence.

::DEVELOPER

Molecular Bioinformatics Center,  National Chiao Tung University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Chang TH, Huang HY, Hsu JB, Weng SL, Horng JT, Huang HD:
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs.
BMC bioinformatics 2013, 14 Suppl 2:S4

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
Huang HY, Chien CH, Jen KH, Huang HD.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34.

fGWAS 2.0 – Functional GWAS software

fGWAS 2.0

:: DESCRIPTION

The fGWAS (Function Genome-wide association study) is a new concept to evaluate additive and dominant effect for every SNP and identify the significant SNPs from huge SNP data

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

fGWAS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 fGWAS

:: MORE INFORMATION

Citation

Hum Genet. 2011 Jun;129(6):629-39. doi: 10.1007/s00439-011-0960-6. Epub 2011 Feb 4.
A dynamic model for genome-wide association studies.
Das K, Li J, Wang Z, Tong C, Fu G, Li Y, Xu M, Ahn K, Mauger D, Li R, Wu R.

BAR+ – Functional and Structural Annotation of Protein sequences

BAR+

:: DESCRIPTION

BAR+ (Bologna Annotation Resource)is a server for the annotation of protein sequences relying on a comparative large-scale genome analysis across 988 species and the entire UniProt. With BAR+ and a sequence/set of sequences (maximum number per run=50) you can annotate when possible: function (Gene Ontology), structure and ligands (Protein Data Bank), structural classification (SCOP), protein domains (Pfam). Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM (HMM profile) that allows you to directly compute your 3D model. Cluster HMMs (over 10.000) are available for downloading.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No, Only Web Service

:: MORE INFORMATION

Citation

Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi and Rita Casadio.
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
NAR – Web server special issue 2011