TAGOPSIN 1.3 – Collating Taxa-specific Gene and Protein Functional and Structural Information

TAGOPSIN 1.3

:: DESCRIPTION

TAGOPSIN (TAxonomy, Gene, Ontology, Protein, Structure INtegrated) retrieves select data from NCBI Taxonomy, NCBI Nucleotide, UniProtKB, Gene Ontology, Pfam, EBI SIFTS and RCSB PDB, and assembles them in the database management system PostgreSQL. TAGOPSIN is an organism-centred data warehousing tool that works with prokaryotic and eukaryotic organisms as well as viruses.

::DEVELOPER

TAGOPSIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Java
PostgreSQL

:: DOWNLOAD

TAGOPSIN

:: MORE INFORMATION

Citation

Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y.
TAGOPSIN: collating taxa-specific gene and protein functional and structural information.
BMC Bioinformatics. 2021 Oct 23;22(1):517. doi: 10.1186/s12859-021-04429-5. PMID: 34688246; PMCID: PMC8541804.

CPhos 1.3 – Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites

CPhos 1.3

:: 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

:: 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.

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

:: 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