tilingArray 1.47.0 – Transcript mapping with high-density oligonucleotide tiling arrays

tilingArray 1.47.0

:: 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.

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.

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.

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.

Primrose 2.17 – Identify Oligonucleotides

Primrose 2.17

:: DESCRIPTION

Primrose is a free program that uses data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Primrose

:: MORE INFORMATION

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.

Spector II – Calculate Concentration of Oligonucleotides based on OD Values

Spector II

:: DESCRIPTION

Spector is a freeware stand-alone program that calculates the concentration of oligonucleotides based on OD values. Values can be printed or collated into a file for pemanent record keeping.

::DEVELOPER

Lawrence’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Spector

:: MORE INFORMATION