Tag: Probe

TIPMaP – Transcript Isoform Profiles from Microarray Probes

TIPMaP

:: DESCRIPTION

TIPMaP is a tool developed to identify differentially regulated transcripts (specific to human, mouse and rat).

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS, Acharya KK.
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
BMC Genomics. 2013 Dec 27;14:922. doi: 10.1186/1471-2164-14-922. PMID: 24373374; PMCID: PMC3884118.

WinXPCNVer – Calculating Vst values between two Populations Probe

WinXPCNVer

:: DESCRIPTION

WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

WinXPCNVer

:: MORE INFORMATION

Citation

Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, Wu S, Yang Y, Li S, Kang L, Guan Y, Hoh BP, Chung YJ, Jin L, Su B, Xu S.
A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence.
Am J Hum Genet. 2015 Jul 2;97(1):54-66. doi: 10.1016/j.ajhg.2015.05.005. Epub 2015 Jun 11. PMID: 26073780; PMCID: PMC4572470.

chipD 1.0 – Design Oligonucleotide Probes for high-density Tiling Arrays

chipD 1.0

:: 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.

AffyRNADegradation 1.38.0 – Analyze and Correct Probe Positional Bias in Microarray data due to RNA Degradation

AffyRNADegradation 1.38.0

:: 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.

FastPCR 6.7.50 – PCR Primers or Probe Design

FastPCR 6.7.50

:: 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.

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.

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

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

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

Kevin Yuk-Lap Yip

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl
  • R Package

:: DOWNLOAD

 ProbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21.
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.

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