Kontaminant – Kmer-based Screening and Filtering tool for Next-gen Sequencing Reads

Kontaminant

:: DESCRIPTION

Kontaminant is a kmer-based screening and filtering tool for next-gen sequencing reads.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Kontaminant

:: MORE INFORMATION

Citation

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Daly, G.M., Leggett, R.M., Rowe, W., Stubbs, S., Wilkinson, M., Ramirez-Gonzalez, R.H., Caccamo, M., Bernal, W., Heeney, J.L.
PLoS One. 2015 Jun 22;10(6):e0129059. doi: 10.1371/journal.pone.0129059

SbacHTS v5 – Spatial background correction for High-Throughput RNAi Screening

SbacHTS v5

:: DESCRIPTION

SbacHTS is a software for visualization, estimation and correction of spatial background noises of RNAi screening experiment results.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SbacHTS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2218-20. doi: 10.1093/bioinformatics/btt358. Epub 2013 Jun 28.
SbacHTS: spatial background noise correction for high-throughput RNAi screening.
Zhong R1, Kim MS, White MA, Xie Y, Xiao G.

ScreenCap3 – Screening of Caspase-3 substrates and Cleavage site prediction

ScreenCap3

:: DESCRIPTION

ScreenCap3 is a web-based prediction method, to facilitate the discovery of novel caspase-3 substrates in human proteome.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2014 Sep;14(17-18):2042-6. doi: 10.1002/pmic.201400002. Epub 2014 Aug 4.
ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites.
Fu SC, Imai K, Sawasaki T, Tomii K.

FastQ Screen 0.7.0 – Screening Application for High Througput Sequence data

FastQ Screen 0.7.0

:: DESCRIPTION

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Perl

:: DOWNLOAD

 FastQ Screen

:: MORE INFORMATION

PSS 20091105 – Protein Profile Similarity Screening

PSS 20091105

:: DESCRIPTION

PSS is a matlab code of computational protein profile similarity screening for quantitative mass spectrometry experiments.

::DEVELOPER

Hamprecht lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 PSS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):77-83. doi: 10.1093/bioinformatics/btp607. Epub 2009 Oct 27.
Computational protein profile similarity screening for quantitative mass spectrometry experiments.
Kirchner M1, Renard BY, Köthe U, Pappin DJ, Hamprecht FA, Steen H, Steen JA.

Fit3D v005 – Small Structural Motif Screening in Proteins and further analyses

Fit3D v005

:: DESCRIPTION

Fit3D is a command line software tool to search for small structural motifs of amino acids in target proteins. It can also be used for batch-processing by applying to a large number of target structures.

::DEVELOPER

Fit3D team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 Fit3D

:: MORE INFORMATION

Citation:

Fit3D – A web application for highly accurate screening of spatial residue patterns in protein structure data.
Kaiser F, Eisold A, Bittrich S, Labudde D.
Bioinformatics. 2015 Oct 30. pii: btv637.

iScreen 1.0 – Image-Based High-content RNAi Screening Analysis Tool

iScreen 1.0

:: DESCRIPTION

iScreen is an R package for the statistical modeling and visualization of image-based high-content RNAi screening.

::DEVELOPER

Rui Zhong <rui.zhong@utsouthwestern.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • R

:: DOWNLOAD

 iScreen

:: MORE INFORMATION

Citation:

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.
Zhong R, Dong X, Levine B, Xie Y, Xiao G.
J Biomol Screen. 2014 Dec 29. pii: 1087057114564348.

FastPros 1.0.0 – Screening of Reaction Knockout Strategies for Metabolic Engineering

FastPros 1.0.0

:: DESCRIPTION

FastPros (Fast algorithm of knockout screening for target Production based on shadow price analysis), a new iterative screening algorithm, which uses biomass production maximization to identify sets of metabolic reactions whose simultaneous knockouts result in the production of a target metabolite

::DEVELOPER

Shimizu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

 FastPros

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):981-7. doi: 10.1093/bioinformatics/btt672. Epub 2013 Nov 19.
FastPros: screening of reaction knockout strategies for metabolic engineering.
Ohno S1, Shimizu H, Furusawa C.

AMMOS / DG-AMMOS – Automated Molecular Mechanics Optimization tool for in silico Screening / using Distance Geometry

AMMOS / DG-AMMOS

:: DESCRIPTION

AMMOS is a package to refine the 3D structures of compounds and of compounds docked into a protein target.

DG-AMMOS is a New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening.

::DEVELOPER

Molécules Thérapeutiques in silico (MTi)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 AMMOS / DG-AMMOS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Oct 16;9:438. doi: 10.1186/1471-2105-9-438.
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA.

BMC Chem Biol. 2009 Nov 13;9:6. doi: 10.1186/1472-6769-9-6.
DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.
Lagorce D, Pencheva T, Villoutreix BO, Miteva MA.

MutScreener – Design Primers for Mutation Screening

MutScreener

:: DESCRIPTION

MutScreener assists in the analysis of human gene structure and design of PCR/sequencing primer.

::DEVELOPER

Dr. Liu’s Laboratories  

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W660-4.
MutScreener: primer design tool for PCR-direct sequencing.
Yao F1, Zhang R, Zhu Z, Xia K, Liu C.