Tag: Validation

ArtiFuse v1.0.0 – Computational Validation of Fusion Gene Detection tools without relying on simulated reads

ArtiFuse v1.0.0

:: DESCRIPTION

ArtiFusion is a tool to simulate artificial fusion events by modifying a given reference genome. The tool copies parts of the exonic sequence of gene A within the reference genome FASTA sequence into the downstream region of gene B and replaces the copied regions of gene A with Ns. The breakpoints are defined by using a size ratio between gene A and gene B and are always placed on exon-exon junctions. Intronic and intergenic regions remain unchanged.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

ArtiFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Aug 2. pii: btz613. doi: 10.1093/bioinformatics/btz613.
ArtiFuse – Computational validation of fusion gene detection tools without relying on simulated reads.
Sorn P, Hohlsträter C, Löwer M, Sahin U, Weber D.

Check My Metal – Metal Binding Site Validation Server

Check My Metal

:: DESCRIPTION

CMM (Check My Metal) is a web server for the validation of metal binding sites in macromolecules.

::DEVELOPER

Minor Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

BioNetCAD 1.1 – Design, Simulation and Experimental Validation of Synthetic Biochemical Networks

BioNetCAD 1.1

:: DESCRIPTION

BioNetCAD ,a CellDesigner plug-in, is a computer assisted design tool for synthetic biology.

::DEVELOPER

BioNetCAD team

:: SCREENSHOTS

BioNetCAD

:: REQUIREMENTS

:: DOWNLOAD

 BioNetCAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
Rialle S1, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F.

IRMa 1.31.1 – Validation of MS Peptides Identification

IRMa 1.31.1

:: DESCRIPTION

IRMa ( Interprétation des Résultats Mascot)  toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches.

::DEVELOPER

Christophe Bruley

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

:: DOWNLOAD

 IRMa

:: MORE INFORMATION

Citation

Veronique Dupierris; Christophe Masselon; Magali Court; Sylvie Kieffer-Jaquinod; Christophe Bruley
A toolbox for Validation of mass spectrometry peptides identification and Generation of database: IRMa
Bioinformatics 2009;25 (15): 1980-1981. doi: 10.1093/bioinformatics/btp301

GeneTerrain – Next-generation Panel Biomarker Discovery and Validation software

GeneTerrain

:: DESCRIPTION

GeneTerrain is a next-generation panel biomarker discovery and validation software.

::DEVELOPER

Discovery Informatics and Computing Laboratory@ Indiana University School of Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Please join the mailing group to obtain instructions for downloading a pre-release version of the software.

:: MORE INFORMATION

Citation

You Qian, Shiaofen Fang, and Jake Y. Chen (2008)
GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks
Information Visualization, doi: 10.1057/palgrave.ivs.9500169

SeqClean 20110222 – Trim & Validation of ESTs or other DNA sequences

SeqClean 20110222

:: DESCRIPTION

SeqClean (Sequence Cleaner) is a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.

::DEVELOPER

The Gene Index Project

:: REQUIREMENTS

:: DOWNLOAD

 SeqClean

:: MORE INFORMATION

Citation:

An optimized procedure greatly improves EST vector contamination removal.
Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI.
BMC Genomics. 2007 Nov 13;8:416.

 

sequins 20070909 – Validation of Sequence Assignment

sequins 20070909

:: DESCRIPTION

‘sequins‘ performs sequence validation by comparing the model side chains against the electron density. It may be run with phases from experimental phasing, or it can calculate its own phases using a side-chain-omit process. In this case it can be used after molecular replacement, or to validate structures in the PDB.

::DEVELOPER

Kevin Cowtan

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  sequins

:: MORE INFORMATION

Exit mobile version