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.

Primer3 - (Found June 29, 2008 )

Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.
http://www.genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi

Primer Z - (Found June 29, 2008 )

Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.
http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

siRNAdb - (Found June 29, 2008 )

This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs).
http://sirna.cgb.ki.se/

siVirus - (Found June 29, 2008 )

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.
http://sivirus.rnai.jp/

WatCut - (Found June 29, 2008 )

WatCut allows you to perform restriction analysis and silent mutation analysis. The restriction analysis results can be displayed as a table or graphically to compare the results of different digests. All commercially available type II restriction enzymes are known. The silent mutation analysis scans your oligonucleotide sequence for restriction sites that could be introduced without altering the protein that is encoded.
http://watcut.uwaterloo.ca/watcut/template.php

VectorNTI - (Found June 29, 2008 )

VectorNTI is an application for integrated for molecular sequence analysis including primer design, virtual cloning, alignments, and sequence assembly. The free license needs to be renewed every year.
https://catalog.invitrogen.com/index.cfm?fuseaction=userGroup.home

Universal Probes - (Found June 29, 2008 )

The Universal Probes (U-Probe) project provides access to a database of pre-computed hybridization-based probes. The probes are based on highly conserved sequences from multiple sequenced species, and can be used to screen genomic libraries for which there is a lack of available species-specific data. The database can be searched on the website, or complete copies can be downloaded. The computer scripts and experimental protocols used in the project are also available for download.
http://uprobe.genetics.emory.edu/

TROD - (Found June 29, 2008 )

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.
http://www.cellbio.unige.ch/RNAi.html

TGGE-STAR - (Found June 29, 2008 )

TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping.
http://www.charite.de/bioinf/tgge/

Stitchprofiles.uio.no - (Found June 29, 2008 )

Stitchprofiles.uio.no is a server that performs web-based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server can also plot the classical melting curves, probability profiles, and temperature profiles.
http://stitchprofiles.uio.no/