Bioinformatics Links Directory : Tools For the Bench

These links contain programs which can create restriction enzyme maps for your sequence of interest. Also included are tools for the design of oligonucleotide probes and PCR primers.

dsCheck - (Found June 29, 2008 )

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.
http://dscheck.rnai.jp/

dnaMATE - (Found June 29, 2008 )

dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available; list of other melting temperature calculation servers also provided.
http://dna.bio.puc.cl/tm.html

DINAMelt - (Found June 29, 2008 )

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.
http://www.bioinfo.rpi.edu/applications/hybrid/

DEQOR - (Found June 29, 2008 )

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.
http://cluster-1.mpi-cbg.de/Deqor/deqor.html

DePIE - (Found June 29, 2008 )

Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.
http://biocore.unl.edu/primer/primerPI.html

CODEHOP - (Found June 29, 2008 )

COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
http://blocks.fhcrc.org/codehop.html

Assembly PCR Oligo Maker - (Found June 29, 2008 )

Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.
http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html

ASePCR - (Found June 29, 2008 )

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.
http://genome.ewha.ac.kr/ASePCR/

Genefisher - (Found June 29, 2008 )

Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.
http://bibiserv.techfak.uni-bielefeld.de/genefisher/

GLUE, PEDEL, and DRIVeR - (Found June 29, 2008 )

GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results.
http://guinevere.otago.ac.nz/mlrgd/STATS/index.html