Tag: Evaluation

ClustEval 1.6 – Integrative Clustering Evaluation Framework

ClustEval 1.6

:: DESCRIPTION

ClustEval is a free and extendable opensource platform for objective performance comparison of arbitrary Clustering Methods on different datasets.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 ClustEval

:: MORE INFORMATION

Citation

Guiding biomedical clustering with ClustEval.
Wiwie C, Baumbach J, Röttger R.
Nat Protoc. 2018 Jun;13(6):1429-1444. doi: 10.1038/nprot.2018.038.

Comparing the performance of biomedical clustering methods.
Wiwie C, Baumbach J, Röttger R.
Nat Methods. 2015 Nov;12(11):1033-8. doi: 10.1038/nmeth.3583.

JMS v1 – Evaluation of Diagnostic Status of Juxtaposed Microsatellite Systems

JMS v1

:: DESCRIPTION

JMS (Juxtaposed microsatellite systems) is a computer program for a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems.

::DEVELOPER

Arnaud Estoup

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 JMS

:: MORE INFORMATION

Citation

Estoup A, Cornuet JM, Rousset F, Guyomard R (1999)
Juxtaposed microsatellite systems as diagnostic markers for admixture: theorical aspects.
Molecular Biology and Evolution, 16, 898-908.

EFIN – Evaluation of Functional Impact of Nonsynonymous SNPs

EFIN

:: DESCRIPTION

EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 10;15:455. doi: 10.1186/1471-2164-15-455.
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome.
Zeng S, Yang J, Chung BH, Lau YL, Yang W

BTEVAL – Evaluation of beta-turn Prediction

BTEVAL

:: DESCRIPTION

The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S. (2003)
BTEVAL: A server for evaluation of beta-turn prediction methods.
Journal of Bioinformatics and Computational Biology 3(1), 495-504.

TCS – Evaluation and Filtering of multiple Sequence Alignments

TCS

:: DESCRIPTION

TCS (Transitive Consistency Score) web server is a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.
Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.
Nucleic Acids Res. 2015 Apr 8. pii: gkv310.

SOESA 0.21b – Structure Optimization and Evaluation using Separations of Atoms

SOESA 0.21b

:: DESCRIPTION

Soesa is a program for use in evaluating and refining atomic models of protein structures. The program calculates an estimated prior probability of the interatomic distances in the structure by reference to an interatomic distance probability density function (PDF) database compiled from known structures. It also calculates derivatives with respect to atomic position vectors for use in molecular dynamics simulations and structure refinement.

::DEVELOPER

Michael Wall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SOESA

:: MORE INFORMATION

Citation

Michael E. Wall, Shankar Subramaniam, and George N. Phillips, Jr.
Protein structure determination using a database of interatomic distance probabilities. 1999.
Protein Science 12:2720-27.

pPIC9 – Evaluation and Design for high-level Expression of Foreign Genes in pPIC9 Vector

pPIC9

:: DESCRIPTION

pPIC9 is a program for evaluation and design for high-level expression of foreign genes in pPIC9 vector

::DEVELOPER

Center of Computational Biology, Beijing Institute of Basic Medical Sciences

:: SCREENSHOTS

pPIC9

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 pPIC9

:: MORE INFORMATION

Citation:

Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification.
Wu B, Cha L, Du Z, Ying X, Li H, Xu L, Zheng X, Li E, Li W.
Biochem Biophys Res Commun. 2007 Mar 9;354(2):498-504

Tagger – Selection and Evaluation of tag SNPs

Tagger

:: DESCRIPTION

Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

P.I.W. de Bakker, R. Yelensky, I. Pe’er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005)
Efficiency and power in genetic association studies.
Nature Genetics. 37: 1217-1223

Bimax – Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data

Bimax

:: DESCRIPTION

 Bimax is asystematic comparison and evaluation of biclustering methods for gene expression data.

::DEVELOPER

 the Systems Optimization Group, Institut TIK, ETH Zürich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 Bimax

:: MORE INFORMATION

Citation

A. Prelic, S. Bleuler, P. Zimmermann, A. Wille, P. Bühlmann, W. Gruissem, L. Hennig, L. Thiele, and E. Zitzler.
A Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data.
Bioinformatics, 22(9):1122–1129, 2006.

TAMEE 1.1 – Tissue Array Management and Evaluation Environment

TAMEE 1.1

:: DESCRIPTION

TAMEE is a web-based database application for the management and analysis of data resulting from the production and experimental use of TMAs. In addition to production and experimental parameters images generated during the different stages of the TMA workflow are stored. Parameter values are based on structured classifications to ensure consistent database content which is the basis to yield biologically meaningful results in subsequent data analysis. Therefore existing public classifications are used and new controlled vocabularies have been defined in the context of the application. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be automatically evaluated with a set of predefined analysis algorithms. Additional algorithms for the evaluation of tissue cores can be added to the application via a plug-in interface. Downstream analysis of the results is facilitated via a set of standard queries. More complex queries can be formulated with the help of a flexible query generator.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  •  MySQL

:: DOWNLOAD

 TAMEE

:: MORE INFORMATION

Citation

Thallinger GG, Baumgartner K, Pirklbauer M, Uray M, Pauritsch E, Mehes G, Buck CR, Zatloukal K, Trajanoski Z.
TAMEE: data management and analysis for tissue microarrays.
BMC Bioinformatics. 2007. 8:81.