FastPCR 6.5.55 – PCR Primers or Probe Design

FastPCR 6.5.55

:: DESCRIPTION

FastPCR software has integrated tools environment that provide comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR) multi-fragments assembling cloning; single primer PCR (design of PCR primers from close located inverted repeat), automatically SSR loci detection and direct PCR primers design, amino acid sequence degenerate PCR, Polymerase Chain Assembly (PCA) or oligos assembly and much more.The “in silico” (virtual) PCR primers or probe searching, comprehensive pairs and individual primers analysis tests are included. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting calculation.

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FastPCR

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1116:271-302. doi: 10.1007/978-1-62703-764-8_18.
FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Kalendar R1, Lee D, Schulman AH.

Kalendar R, Lee D, Schulman AH 2009.
FastPCR Software for PCR Primer and Probe Design and Repeat Search.
Genes, Genomes and Genomics, 3(1): 1-14.

Re-Annotator 1.0.0 – Re-annotates Microarray Probes

Re-Annotator 1.0.0

:: DESCRIPTION

Re-Annotator is a re-annotation pipeline for gene expression microarrays that will bring probe annotations up-to-date!

::DEVELOPER

André Altmann

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl, BWA,SAMtools,Annovar

:: DOWNLOAD

  Re-Annotator

:: MORE INFORMATION

Citation

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.
Arloth J, Bader DM, Röh S, Altmann A.
PLoS One. 2015 Oct 1;10(10):e0139516. doi: 10.1371/journal.pone.0139516

ProbRNA 20131213 – Modeling RNA Structure Probing data

ProbRNA 20131213

:: DESCRIPTION

ProbRNA produces features found to be related to both the secondary and tertiary structures of the RNAs.

::DEVELOPER

Hong Kong Bioinformatics Center, The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl
  • R Package

:: DOWNLOAD

 ProbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21. [Epub ahead of print]
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
Hu X1, Wong TK, Lu ZJ, Chan TF, Lau TC, Yiu SM, Yip KY.

AffyRNADegradation 1.14.0 – Analyze and Correct Probe Positional Bias in Microarray data due to RNA Degradation

AffyRNADegradation 1.14.0

:: DESCRIPTION

AffyRNADegradation helps with the assessment and correction of RNA degradation effects in Affymetrix 3′ expression arrays.

::DEVELOPER

Mario Fasold <fasold at izbi.uni-leipzig.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • R
  • BioConductor

:: DOWNLOAD

 AffyRNADegradation

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):129-31. doi: 10.1093/bioinformatics/bts629. Epub 2012 Oct 24.
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
Fasold M1, Binder H.

METCAP – Probe Generation Tool for Large-scale Targeted Metagenomics Sequence Capture

METCAP

:: DESCRIPTION

MetCap is a web-based tool that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies.

::DEVELOPER

MetCap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.
Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D.
BMC Bioinformatics. 2015 Feb 28;16(1):65.

chipD – Design Oligonucleotide Probes for high-density Tiling Arrays

chipD

:: DESCRIPTION

The chipD Server is a tool for designing ChIP-chip microarrays with full genome coverage or to design expression arrays.

::DEVELOPER

UW BACTER Institute 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 chipD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W321-5. doi: 10.1093/nar/gkq517. Epub 2010 Jun 6.
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.
Dufour YS1, Wesenberg GE, Tritt AJ, Glasner JD, Perna NT, Mitchell JC, Donohue TJ.

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

artefactCorrection 1.1 – Detection and Correction of Probe-level Artefacts on microarrays

artefactCorrection 1.1

:: DESCRIPTION

artefactCorrection is a simple approach to detect artefacts with high recall and precision which we further improve by taking into account the spatial layout of arrays.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 artefactCorrection

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 30;13:114. doi: 10.1186/1471-2105-13-114.
Detection and correction of probe-level artefacts on microarrays.
Petri T, Berchtold E, Zimmer R, Friedel CC.

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