OligoCalc 3.26 – Oligonucleotide Properties Calculator

OligoCalc 3.26

:: DESCRIPTION

OligoCalc is a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation.

::DEVELOPER

Warren A. Kibbe, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 OligoCalc

:: MORE INFORMATION

Citation

Kibbe WA.
OligoCalc: an online oligonucleotide properties calculator‘. (2007)
Nucleic Acids Res. 35(webserver issue): May 25.

Ex-Ex Primer – Designing Oligonucleotides Spanning Spliced Nucleic Acid Regions

Ex-Ex Primer

:: DESCRIPTION

Ex-Ex Primer is a new computational program which offers many improved, user-friendly features, and reliably creates junction primers and probes.

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Govindkumar B, Kavyashree B, Patel K, Sasidharan K, T SA, Thomas L, Bkg P, Hn R, R M, Acharya KK.
Ex-Ex Primer: an experimentally validated tool for designing oligonucleotides spanning spliced nucleic acid regions from multiple species.
J Biotechnol. 2021 Oct 28:S0168-1656(21)00277-7. doi: 10.1016/j.jbiotec.2021.10.009. Epub ahead of print. PMID: 34756973.

ProbeMatch – Rapid Alignment of Oligonucleotides to Genome

ProbeMatch

:: DESCRIPTION

ProbeMatch is a sequence alignment program designed for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike existing tools such as ELAND and MAQ which only perform ungapped alignments allowing at most 2-3 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 errors including insertion, deletion, and mismatch.

::DEVELOPER

Jignesh M. Patel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 ProbeMatch

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Kim YJ1, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

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.

d2SBin v1.0 – Improving the Binning of Metagenomic Contigs on d2S Oligonucleotide Frequency Dissimilarity

d2SBin v1.0

:: DESCRIPTION

d2SBin is easy-to-use contig-binning improving tool, which adjusted the contigs among bins based on the output of any existing binning tools. The tool is taxonomy-free only on the k-tuples for single metagenomic sample.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Python

:: DOWNLOAD

d2SBin

:: MORE INFORMATION

Citation

Wang Y, Wang K, Lu YY, Sun F.
Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity.
BMC Bioinformatics. 2017 Sep 20;18(1):425. doi: 10.1186/s12859-017-1835-1. PMID: 28931373; PMCID: PMC5607646.

tilingArray 1.71.0 – Transcript mapping with high-density oligonucleotide tiling arrays

tilingArray 1.71.0

:: DESCRIPTION

tilingArray provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  tilingArray

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20.
Transcript mapping with high-density oligonucleotide tiling arrays.
Huber W, Toedling J, Steinmetz LM.

BOND – Basic OligoNucleotide Design

BOND

:: DESCRIPTION

BOND is a program for designing DNA oligonucleotides. In comprehensive testing, it achieved 100% sensitivity and specificity.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BOND

:: MORE INFORMATION

Citation

BOND: Basic OligoNucleotide Design.
Ilie L, Mohamadi H, Golding GB, Smyth WF.
BMC Bioinformatics. 2013 Feb 27;14:69. doi: 10.1186/1471-2105-14-69.

OligoFaktory SE – Oligonucleotide Design

OligoFaktory SE

:: DESCRIPTION

OligoFaktory Standalone Edition is a free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more…

::DEVELOPER

Colas Schretter

:: SCREENSHOTS

OligoFaktory

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 OligoFaktory

:: MORE INFORMATION

Citation

Bioinformatics (2006) 22 (1): 115-116.
OLIGOFAKTORY: a visual tool for interactive oligonucleotide design
Colas Schretter and Michel C. Milinkovitch

OligoCounter 0.64 – Count Overrepresented 8-14bp Oligonucleotides in DNA Sequences

OligoCounter 0.64

:: DESCRIPTION

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example from metagenomics) to a sequenced genome.

OligoViz : allows direct visualisation of OligoCounter data

OligoWords : generates 4mer data for JCircleGraph (use the perl script to extract 4mer data from a fasta file).

JCircleGraph : visualisation of 4mer and OligoCounter data in attractive genome atlases (requires 4mer files from OligoWords!).

::DEVELOPER

Dr Colin F. Davenport

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 OligoCounter

:: MORE INFORMATION

Citation

Davenport, C. F., Wiehlmann, L., Reva, O. N. & Tümmler, B.
Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides.
Environ Microbiol. 2009 May;11(5):1092-104.