RepeatMasker 4.0.6 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences

RepeatMasker 4.0.6

:: DESCRIPTION

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

::DEVELOPER

RepeatMasker Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatMasker

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1362-8. Epub 2008 May 23.
DupMasker: a tool for annotating primate segmental duplications.
Jiang Z, Hubley R, Smit A, Eichler EE.

RNAither 2.18.0 – Statistical analysis of high-throughput RNAi screens

RNAither 2.18.0

:: DESCRIPTION

RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.

::DEVELOPER

Lars Kaderali <lars.kaderali at tu-dresden.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 RNAither

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):678-9. doi: 10.1093/bioinformatics/btp014. Epub 2009 Jan 25.
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.
Rieber N1, Knapp B, Eils R, Kaderali L.

ScreenBEAM 1.0 – Functional Genomics Screens via Bayesian Hierarchical Modeling

ScreenBEAM 1.0

:: DESCRIPTION

ScreenBEAM is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported

::DEVELOPER

Jiyang Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 ScreenBEAM

:: MORE INFORMATION

Citation

ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.
Yu J, Silva J, Califano A.
Bioinformatics. 2015 Sep 28. pii: btv556.

Super 20130207 – Screen Superposable Oligopeptide Fragments from PDB

Super 20130207

:: DESCRIPTION

Super is a web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank

::DEVELOPER

Laboratory of Computational Biology (LCB), Monash University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  Super

:: MORE INFORMATION

Citation:

James H. Collier, Arthur M. Lesk, Maria Garcia de la Banda and Arun S. Konagurthu,
Super: A web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank.
Nucleic Acids Research 40(W1): W334-W339, July 2012.

imageHTS 1.19.0 – Analysis of high-throughput Microscopy-based Screens

imageHTS 1.19.0

:: DESCRIPTION

imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  imageHTS

:: MORE INFORMATION

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Diaz Lab , Jun S. Song’s Research Group

:: SCREENSHOTS

HiTSelect

:: REQUIREMENTS

  • Windows /Linux/ MacOsX

:: DOWNLOAD

 HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.

AutoDimer 1.0 – Screening Tool for Primer-dimer & Hairpin Structures

AutoDimer 1.0

:: DESCRIPTION

AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). AutoDimer was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.

AutoDimer Online Version

::DEVELOPER

Peter M. Vallone

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AutoDimer

:: MORE INFORMATION

Citation

Vallone, P.M. and Butler, J.M. (2004)
AutoDimer: a screening tool for primer-dimer and hairpin structures.
Biotechniques, 37(2): 226-231.

Grid Cell Counter 0.9.9 – Count the Cells Shown on Computer Screen

Grid Cell Counter 0.9.9

:: DESCRIPTION

Grid Cell Counter is a freeware biology tool that will help you to manually count the cells shown on computer screen by displaying a transparent or semi-transparent grid over your image.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Grid Cell Counter

:: MORE INFORMATION

TinT – Screening for Nested Transpositions from Genome Assemblies or Trace data

TinT

:: DESCRIPTION

TinT (Transposition in Transposition) affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window / MacOsX
  • Java

:: DOWNLOAD

 TinT

:: MORE INFORMATION

Citation

Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J. (2010)
A Novel Web-Based TinT Application and the Chronology of the Primate Alu Retroposon Activity.
BMC Evolutionary Biology 10:376.

POBO 20050518 – Screen predetermined Cis-elements from a set of sequences

POBO 20050518

:: DESCRIPTION

POBO is a tool to summarize, verify and screen predetermined cis-elements from a set of sequences. POBO reports the results in as understandable format as possible for biologists.After finding the regulatory elements, it can be helpful to summarize the statistics into as readable format as possible or to do more intensive analyses. POBO enables rapid evaluation of pre-defined regulatory elements and can therefore be used to verify hypothesis.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  POBO

:: MORE INFORMATION

Citation:

Kankainen,M. and Holm,L. (2004)
POBO, transcription factor binding site verification with bootstrapping.
Nucleic Acids Research, 32(Web Server issue), W222-W229.