nondetects 2.16.0 – Model and Impute non-detects in qPCR data

nondetects 2.16.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

PhiSiGns 1.2 – Indentify Signature Genes in Phages and Design Primers

PhiSiGns 1.2

:: DESCRIPTION

PhiSiGns is a web-based and standalone application that provides a simple and convenient tool to identify signature genes and design primers for PCR amplification of related genes from environmental samples. PhiSiGns is intended for phage biologists who want to find common conserved genes in phages for evolution or phylogeny based studies, or who are interested in designing primers that can be used to explore environmental phage diversity.

PhiSiGns Online Version

::DEVELOPER

the Breitbart lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhiSiGns

:: MORE INFORMATION

Citation:

Bhakti Dwivedi, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards, and Mya Breitbart (in review)
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
BMC Bioinformatics 2012, 13:37

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

AMUSER 1.0 – Design of Optimal PCR Primers for USER Cloning

AMUSER 1.0

:: DESCRIPTION

AMUSER (Automated DNA Modifications with USER cloning) offers quick and easy design of PCR primers optimized for various USER cloning based DNA engineering

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly.
Genee HJ, Bonde MT, Bagger FO, Jespersen JB, Sommer MO, Wernersson R, Olsen LR.
ACS Synth Biol. 2015 Mar 20;4(3):342-9. doi: 10.1021/sb500194z.

ProbeSpec – Map Specificity of all Candidate Probes for a Given Sequence

ProbeSpec

:: DESCRIPTION

ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProbeSpec

:: MORE INFORMATION

Citation

Doron Lipson, Peter Web, Zohar Yakhini (2002)
Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome
WABI ’02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics

HYDEN – A software for Designing Degenerate Primers

HYDEN

:: DESCRIPTION

HYDEN (HighlY DEgeNerate primers) is a program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp).

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HYDEN

:: MORE INFORMATION

Citation

Degenerate primer design: theoretical analysis and the HYDEN program.
Linhart C, Shamir R.
Methods Mol Biol. 2007;402:221-44.

pcrcoal 1.2.0 – Coalescent Simulations of PCR

pcrcoal 1.2.0

:: DESCRIPTION

pcrcoal is an R package implementing the coalescent approach to PCR simulation

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 pcrcoal

:: MORE INFORMATION

Citation:

Weiss, G, von Haeseler, A (1997)
A coalescent approach to the polymerase chain reaction.
NAR 25(15): 3082-3087

QDD 3.1.2 / QDD-VM 3.1.2 – Select Microsatellite Markers and Design Primers

QDD 3.1.2 / QDD-VM 3.1.2

:: DESCRIPTION

QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input.

QDD-VM (QDD in a virtual machine) is an easy but greedy installation. The virtual machine (VM) comes with QDD and (almost) all its dependencies installed in a Galaxy server.

::DEVELOPER

Emese Meglécz and Jean-François Martin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 QDD / QDD-VM

:: MORE INFORMATION

Citation

Meglécz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N., Martin, J.F. 2010.
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.
Bioinformatics 2010; Vol. 26,3 : 403-404; doi: 10.1093/bioinformatics/btp670.

QUALITY 1.1.6 – Variant of the minimum Chi-squared method for limiting Dilution Assays

QUALITY 1.1.6

:: DESCRIPTION

The program QUALITY is a variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

QUALITY

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 QUALITY

:: MORE INFORMATION

Citation

AIDS Res Hum Retroviruses. 1997 Jun 10;13(9):737-42.
Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays.
Rodrigo AG1, Goracke PC, Rowhanian K, Mullins JI.

PolyMarker – Fast Polyploid Primer Design Pipeline

PolyMarker

:: DESCRIPTION

PolyMarker is a tool that simplifies the design of genetic markers, a laboratory test to know if certain variant of the genome is present or not in a plant.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069.