Tag: High Throughput

WHAM 0.1.5 – High-throughput Sequence Alignment

WHAM 0.1.5

:: DESCRIPTION

WHAM (WISCONSIN’S HIGH-THROUGHPUT ALIGNMENT METHOD) is a high-throughput sequence alignment tool developed at University of Wisconsin-Madison. It aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques.

::DEVELOPER

Jignesh M. Patel 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WHAM

:: MORE INFORMATION

Citation:

WHAM: A High-throughput Sequence Alignment Method,
Y. Li, A. Terrel and J. M. Patel,
SIGMOD 2011, Athens, Greece

SULDEX 0.01 – Simultaneous Ultra high throughput Ligand Dissociation EXperiment

SULDEX 0.01

:: DESCRIPTION

The SULDEX packages is designed to use high throughput sequencing to simultaneously analyze binding dissociation constants for large repertoires of sequences.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SULDEX

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e26105. doi: 10.1371/journal.pone.0026105. Epub 2011 Nov 1.
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.
Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ.

HTqPCR 1.13.0 – Analysis of High-throughput Quantitative Real-time PCR data

HTqPCR 1.13.0

:: DESCRIPTION

HTqPCR, a package for the R statistical computing environment, is a software to enable the processing and analysis of qPCR data across multiple conditions and replicates.

::DEVELOPER

Bertone Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HTqPCR

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Dec 15;25(24):3325-6. Epub 2009 Oct 6.
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Dvinge H, Bertone P.

BDVAL 1.2 – Biomarker Discovery in High-throughput datasets

BDVAL 1.2

:: DESCRIPTION

BDVAL ( Biomarker Discovery and VALidation ) is an open source project for biomarker discovery in high-throughput datasets.

::DEVELOPER

Campagne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  •  Java

:: DOWNLOAD

 BDVAL

:: MORE INFORMATION

Citation:

Dorff KC, Chambwe N, Srdanovic M, Campagne F.
BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets.
Bioinformatics. 2010 Oct 1;26(19):2472-3. Epub 2010 Aug 11

HTPheno – Image Analysis Pipeline for High-Throughput Phenotyping

HTPheno

:: DESCRIPTION

HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening.

::DEVELOPER

HTPheno Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 HTPheno

:: MORE INFORMATION

Citation

A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein and F. Schreiber.
HTPheno: An Image Analysis Pipeline for High-Throughput Plant Phenotyping.
BMC Bioinformatics, 12:e148, 2011.

SNP HiTLink 1.5.1 – SNP High-Throughput Linkage Analysis System

SNP HiTLink 1.5.1

:: DESCRIPTION

SNP HiTLink (SNP High-Throughput Linkage Analysis System)is a computer program providing a useful pipeline to directly connect SNP (Single Nucleotide Polymorphism) data and linkage analysis program.

::DEVELOPER

Dynacom

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
:: DOWNLOAD

 SNP HiTLink

:: MORE INFORMATION

Citation

Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S.
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
BMC Bioinformatics. 2009 Apr 24;10(1):121.

Ortholuge 0.8 – Improve Specificity of High-throughput Ortholog Prediction

Ortholuge 0.8

:: DESCRIPTION

Ortholuge is a computational method that can generate precise ortholog predictions between two species on a genome-wide scale (using additional outgroup data for reference). It can either evaluate a previously constructed set of orthologs or it can generate an initial tentative set of orthologs that are subsequently evaluated. Precise ortholog prediction is important for a variety of analyses that utilize comparative genomics, including regulatory element identification.

::DEVELOPER

Brinkman Laboratory, Simon Fraser University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Ortholuge

:: MORE INFORMATION

Citation

Fulton DL, Li YY, Laird M, Horsman BGS, Roche FMR, Brinkman FSL.
Improving the specificity of high-throughput ortholog prediction.
BMC Bioinformatics, 2006. 7:270.

VcPpt – Protein Ligend Docking & in silico High-throughput Screening

VcPpt

:: DESCRIPTION

VcPpt is an independently developed extension for Vina, a program for flexible ligand docking under Windows OS.Carry out high-throughput screening of compound libraries with Vina and cluster resulting PDB files of ligands by binding energies and by binding positions. Results processing functions do not require Vina installed. Screening scale is unlimited.

::DEVELOPER

BiochemLabSolutions.com

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 VcPpt

:: MORE INFORMATION

RAT 1.0 – Recombination Analysis Tool for High Throughput Analysis of Genomic Sequence

RAT 1.0

:: DESCRIPTION

RAT (Recombination Analysis Tool)is an uncomplicated and intuitive cross-platform Java-based application intended for high-throughput, distance-based analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats. All of RAT’s operations are carried out through GUI’s, and all output can be saved as data files (.txt, .xls, .csv), or .jpg files in the case of graphical outputs. RAT is intuitive and easy to use, and only requires a minimum of input from the user. All the parameters have default values, all of which may be changed by the user.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

  RAT 

:: MORE INFORMATION

Citation:

Etherington GJ, Dicks J and Roberts IN (2005)
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.
Bioinformatics 21(3):278-281.

ORFprimer 1.6.4.1 – High Throughput PCR Primer Design

ORFprimer 1.6.4.1

:: DESCRIPTION

ORFprimer is an extended software package for high throughput PCR primer design for biological sequences.ORFprimer can be used to compute primers for up to thousands of target sequences.This procedure can be automated furthermore by reading the targets through text files.

::DEVELOPER

Konrad Büssow and Steve Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ORFprimer

:: MORE INFORMATION