Tag: PROBER

PROBer v0.3.1 – Toolkit for Analyzing Sequencing-based ‘Toeprinting’ Assays

PROBer v0.3.1

:: DESCRIPTION

PROBer is the first unified probabilistic framework for the analysis of a diverse set of sequencing-based ‘toeprinting’ assays. These assays are used to probe RNA secondary structure (DMS/SHAPE-Seq), detect epitranscriptomic mark (Pseudo-Seq), or identify RNA-protein interaction (iCLIP/eCLIP), which are important to understanding post-transcriptional gene regulation from all aspects.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

PROBer

:: MORE INFORMATION

Citation

Cell Syst, 4 (5), 568-574.e7 2017 May 24
PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays
Bo Li , Akshay Tambe , Sharon Aviran , Lior Pachter

PROBER 2.1 – Fish Oligo Probe Design Software

PROBER 2.1

:: DESCRIPTION

PROBER is an oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals.  Generating Tiling Oligonucleotide Probes (TOPs) requires software capable of masking repetitive genomic sequences and saturating unique contiguous blocks with small (100-2000bp), DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.

::DEVELOPER

Nicholas Navin

:: SCREENSHOTS

PROBER

:: REQUIREMENTS

  • Windows
  • .net framework

:: DOWNLOAD

 PROBER

:: MORE INFORMATION

Citation

Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Maner S, Sebat J, Zetterberg A, Wigler M.
PROBER : oligonucleotide FISH probe design software.
Bioinformatics. 2006 Jun 1. Epub PMID: 16740623