SurvMicro v0.9 – Assessment of Prognostic miRNA Signatures

SurvMicro v0.9

:: DESCRIPTION

SurvMicro is a free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis.

::DEVELOPER

SurvMicro team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1630-2. doi: 10.1093/bioinformatics/btu087. Epub 2014 Feb 11.
SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis.
Aguirre-Gamboa R, Trevino V.

Survcomp 1.40.0 – Performance Assessment and Comparison for Survival Analysis

Survcomp 1.40.0

:: DESCRIPTION

Survcomp is an R package providing functions to assess and to compare the performance of risk prediction (survival) models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R/Bioconductor

:: DOWNLOAD

Survcomp

:: MORE INFORMATION

Citation:

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.
Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511.

ModFOLD 6 – Model Quality Assessment Server

ModFOLD 6

:: DESCRIPTION

The ModFOLD server is the latest version of server for the estimation of both the global and local (per-residue) quality of 3D protein models.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ModFOLD

:: MORE INFORMATION

Citation

Maghrabi, A.H.A. & McGuffin, L.J. (2017)
ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins,
Nucleic Acids Res. 2017 Jul 3;45(W1):W416-W421. doi: 10.1093/nar/gkx332.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W368-72. doi: 10.1093/nar/gkt294. Epub 2013 Apr 25.
The ModFOLD4 server for the quality assessment of 3D protein models.
McGuffin LJ1, Buenavista MT, Roche DB.

NVT 1.0 – R package for the Assessment of RNA-Seq Normalization methods

NVT 1.0

:: DESCRIPTION

NVT (NORMALIZATION VISUALIZATION TOOL) is an R package for the assessment of RNA-Seq normalization methods.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

NVT

:: MORE INFORMATION

Citation:

Bioinformatics, 32 (23), 3682-3684 2016 Dec 1
NVT: A Fast and Simple Tool for the Assessment of RNA-seq Normalization Strategies
Thomas Eder, Florian Grebien, Thomas Rattei

MAìSTAS – Modeling and Assessment of ISoforms Through Automated Server

MAìSTAS

:: DESCRIPTION

Maìstas is a fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms. The server builds, when possible, comparative structural models for all the splicing isoforms of a submitted gene or set of genes. The models are then analysed in terms of their suitability to exist in the monomeric state, i.e. when a warning appears in the model assessment, it cannot be excluded the possibility that other multimeric state may stabilize the structure.

::DEVELOPER

MAìSTAS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1625-9. doi: 10.1093/bioinformatics/btr198. Epub 2011 Apr 15.
MAISTAS: a tool for automatic structural evaluation of alternative splicing products.
Floris M1, Raimondo D, Leoni G, Orsini M, Marcatili P, Tramontano A.

mRIN 1.2.0 – direct Assessment of mRNA integrity from RNA-Seq data

mRIN 1.2.0

:: DESCRIPTION

mRIN (mRNA integrity number) is a computational method to assess a quantitative measure of mRNA integrityta. This is done by quantitatively modeling of the 3′ bias of read coverage profiles along each mRNA transcript. A per-sample summary mRIN is then derived as an indicator of mRNA degradation. This method has been used for systematic analysis of large scale RNA-Seq data of postmortem tissues, in which RNA degradation during tissue collection is particularly an issue.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Perl

:: DOWNLOAD

mRIN

:: MORE INFORMATION

Citation

Nat Commun. 2015 Aug 3;6:7816. doi: 10.1038/ncomms8816.
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.
Feng H, Zhang X, Zhang C

T-lex 2.2.2 – Assessment of Transposable Element Presence in Next-generation Sequencing data

T-lex 2.2.2

:: DESCRIPTION

The T-lex pipeline identifies reads that indicate the presence or absence of individual TEs with high specificity. Handling a large amount of data, it can return the frequency of a TE in the population.

::DEVELOPER

The Petrov Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

T-lex

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Fiston-Lavier AS, Barrón MG, Petrov DA, González J

Fiston-Lavier AS, Carrigan M, Petrov DA and Gonzalez J.
T-LEX: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Nuc. Acids. Res. 2011 Mar 1;39(6):e36. Epub 2010 Dec 21

MEDUSA – Selection and Visual Assessment of PCR Primer Pair

MEDUSA

:: DESCRIPTION

MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python

MEDUSA

:: MORE INFORMATION

Citation

Bioinformatics. 2001 Jul;17(7):656-7.
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.
Podowski RM, Sonnhammer EL.

COMPASS 3.1 – COmparison of Multiple Protein Sequence Alignments with assessment of Statistical Significance.

COMPASS 3.1

:: DESCRIPTION

COMPASS runs a search with submitted alignment (or sequence) as a query against a database of protein families.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

COMPASS

:: MORE INFORMATION

Citation:

R.I. Sadreyev, M. Tang, B. Kim and N.V. Grishin (2009)
COMPASS server for homology detection: improved statistical accuracy, speed, and functionality.
Nucleic Acids Res doi:10.1093/nar/gkp360.