pFlexAna 0.1.1 – Protein Flexibility Analyzer

pFlexAna 0.1.1

:: DESCRIPTION

The pFlexAna  detects and displays conformational changes in remotely related proteins, without relying on sequence homology

::DEVELOPER

M2AP Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 pFlexAna

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W246-51. doi: 10.1093/nar/gkn259.
pFlexAna: detecting conformational changes in remotely related proteins.
Nigham A, Tucker-Kellogg L, Mihalek I, Verma C, Hsu D.

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)

MSA 4.05 – Microsatellite Analyzer

MSA 4.05

:: DESCRIPTION

The MSA software tool was designed to handle large microsatellite data sets. To avoid error prone reformatting, MSA uses a simple input format, very close to a simple spreadsheet.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 MSA

:: MORE INFORMATION

Citation:

Dieringer, Daniel & Schlötterer, Christian (2003)
Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets.
Molecular Ecology Notes 3 (1), 167-169

PDA 1.0.3 – Phylogenetic Diversity Analyzer

PDA 1.0.3

:: DESCRIPTION

PDA (Phylogenetic Diversity Algorithm)  is a software tool to analyze various aspects of PD and PD-related measures based on both phylogenetic trees and networks

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 PDA

:: MORE INFORMATION

Citation:

Split diversity in constrained conservation prioritization using integer linear programming.
Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A.
Methods Ecol Evol. 2015 Jan;6(1):83-91.

Pro-Maya – Protein Mutant stAbilitY Analyzer

Pro-Maya

:: DESCRIPTION

Pro-Maya predicts the protein stability free energy difference (ΔG), arising from a single-site amino acid substitution compared to the wild-type, denoted as ΔΔG.

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 1;27(23):3286-92. doi: 10.1093/bioinformatics/btr576. Epub 2011 Oct 13.
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site.
Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N.

SDA 1.0 beta – Statistical DIGE Analyzer

SDA 1.0 beta

:: DESCRIPTION

The SDA is a Java-application for the statistical analysis of data from 2-Dimensional Difference Gel Electrophoresis (DIGE).

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

sda

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 SDA

:: MORE INFORMATION

C2Analyzer – Cotarget-Cofunction Analyzer

C2Analyzer

:: DESCRIPTION

The C2Analyzer: Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched.

::DEVELOPER

C2Analyzer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

C2Analyzer: Co-target-co-function analyzer.
Aftabuddin M, Mal C, Deb A, Kundu S.
Genomics Proteomics Bioinformatics. 2014 Jun;12(3):133-6. doi: 10.1016/j.gpb.2014.03.003.

PROVEAN 1.1.5 – Protein Variation Effect Analyzer

PROVEAN 1.1.5

:: DESCRIPTION

PROVEAN is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

::DEVELOPER

PROVEAN Team, J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PROVEAN

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 6. pii: btv195.
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Choi Y, P Chan A

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.
Predicting the functional effect of amino acid substitutions and indels.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

mirnaTA 1.2.3 – miRNA Temporal Analyzer

mirnaTA 1.2.3

:: DESCRIPTION

mirnaTA is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies.

::DEVELOPER

mirnaTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 mirnaTA

:: MORE INFORMATION

Citation:

miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation.
Cer RZ, Herrera-Galeano JE, Anderson JJ, Bishop-Lilly KA, Mokashi VP.
Gigascience. 2014 Oct 13;3:20. doi: 10.1186/2047-217X-3-20.

AnCorr – Genome Track Analyzer

AnCorr

:: DESCRIPTION

AnCorr is the set of tools for genome-wide study of genomic features and their correlations.The tools is designed to compare genome tracks by robust method with their attribution relative to DNA strands.

::DEVELOPER

AnCorr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.
Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI.
DNA Res. 2015 Feb;22(1):109-19. doi: 10.1093/dnares/dsu044.