Tag: Probe

Probe 2.16 – Evaluate Atomic Packing & Contact Analysis

Probe 2.16

:: DESCRIPTION

Probe allows one to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Probe

:: MORE INFORMATION

For a detailed description see Word, et al. (1999), “Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms” J. Mol. Biol. 285, 1709-1731. (download arrow PDF, 1.4MB)

KaPPA-Average 1.0 – Convert Probe ID-based Gene Expression data to Gene ID-based Data

KaPPA-Average 1.0

:: DESCRIPTION

KaPPA-Average organizes such a multiple to multiple relationships between probe IDs and gene IDs, and processes probe ID-based gene expression data to convert to gene ID-based data. When a gene is detectable by several probes, the expression value of the gene is calculated as the average of the probe values.

::DEVELOPER

Kazusa DNA Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  KaPPA-Average

:: MORE INFORMATION

PLATA 1.01 – Probe Level Alternative Transcript Analysis

PLATA 1.01

:: DESCRIPTION

PLATA are the Python scripts for the analyses and visualization of probe level Affymetrix exon array data.

::DEVELOPER

Sandberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 PLATA

:: MORE INFORMATION

Citation

Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites.
Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB.
Science. 2008 Jun 20;320(5883):1643-7.

F-SCAN 1.3 – Fluorescently Probed cDNA Microarray Analysis

F-SCAN 1.3

:: DESCRIPTION

F-SCAN is a software of Fluorescently Probed cDNA Microarray Analysis

::DEVELOPER

Analytical Biostatistics Section,NIH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 F-SCAN

:: MORE INFORMATION

Citation:

A. J. Carlisle, V. V. Prabhu, A. Elkahloun, J. Hudson, J. M. Trent, W. M. Linehan, E. D. Williams, M. R. Emmert-Buck, L. A. Liotta, P. J. Munson, and D. B. Krizman;
“Development of a Prostate cDNA Microarray and Statistical Gene Expression Analysis Package“;
Molecular Carcinogenesis 28:12-22 (2000)

ArrayOligoSelector 3.8.4 – Design Gene Specific Long Oligonucleotide Probes

ArrayOligoSelector 3.8.4

:: DESCRIPTION

ArrayOligoSelector is a software to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3′ end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum

::DEVELOPER

Jingchun Zhu, Zbynek Bozdech, Joe DeRisi, DeRisi Lab, UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  ArrayOligoSelector

:: MORE INFORMATION

Citation:

Zbynek Bozdech et al.
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
Genome Biology 2003 4:R9

ProbeWithO 0.9.0 – Use Small Probe Contact Dots Within O

ProbeWithO 0.9.0

:: DESCRIPTION

ProbeWithO incorporates all-atom contacts into the popular model building program O. An O macro and an unix shell script conduit the dot information between Probe and O to give “almost” interactive updates of clashes.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

ProbeWithO

:: MORE INFORMATION

ProbeWithO is free software available under the terms of its own BSD-style license.