Tag: screening

CRISPR-SURF 1.0 – Screening of Uncharacterized Region Function

CRISPR-SURF 1.0

:: DESCRIPTION

CRISPR-SURF is an exploratory and interactive computational framework for the design and analysis of CRISPR-Cas, CRISPRi, and CRISPRa tiling screens.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • Docker

:: DOWNLOAD

CRISPR-SURF

:: MORE INFORMATION

Citation

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L.
CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.
Nat Methods. 2018 Dec;15(12):992-993. doi: 10.1038/s41592-018-0225-6. PMID: 30504875; PMCID: PMC6620603.

MULTIPRED2 – large-scale Screening of allele-, genotype-, and supertype-specific HLA Associated Peptides

MULTIPRED2

:: DESCRIPTION

MULTIPRED2 is a computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.

::DEVELOPER

MULTIPRED2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

J Immunol Methods. 2011 Nov 30;374(1-2):53-61. doi: 10.1016/j.jim.2010.11.009. Epub 2010 Dec 2.
MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles.
Zhang GL1, DeLuca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V.

FastQ Screen v0.15.0 – Screening Application for High Througput Sequence data

FastQ Screen v0.15.0

:: 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

Citation

Wingett SW, Andrews S.
FastQ Screen: A tool for multi-genome mapping and quality control.
F1000Res. 2018 Aug 24;7:1338. doi: 10.12688/f1000research.15931.2. PMID: 30254741; PMCID: PMC6124377.

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.

CRISPRCloud2 – Deconvolution of your CRISPR pooled screening data

CRISPRCloud2

:: DESCRIPTION

CRISPRCloud2 is a user-friendly cloud-based analysis platform for the deconvolution of CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats) pooled screening data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z.
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.
Bioinformatics. 2017 Sep 15;33(18):2963-2965. doi: 10.1093/bioinformatics/btx335. PMID: 28541456; PMCID: PMC5870715.

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.

AMMOS 2 – Automated Molecular Mechanics Optimization tool for in silico Screening / using Distance Geometry

AMMOS 2

:: DESCRIPTION

AMMOS  (Automatic Molecular Mechanics Optimization for in silico Screening) employs an automatic procedure for energy minimization of protein-ligands complexes.

::DEVELOPER

Molécules Thérapeutiques in silico (MTi)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Server

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Labbé CM, Pencheva T, Jereva D, Desvillechabrol D, Becot J, Villoutreix BO, Pajeva I, Miteva MA.
AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.
Nucleic Acids Res. 2017 May 9.

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.

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.

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.