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.

PDA - (Found June 29, 2008 )

Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.
http://dbb.nhri.org.tw/primer/

PARSESNP - (Found June 29, 2008 )

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.
http://www.proweb.org/parsesnp/

OligoWiz - (Found June 29, 2008 )

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.
http://www.cbs.dtu.dk/services/OligoWiz2/

Oligodb - (Found June 29, 2008 )

Oligodb generates oligos suitable for expression experiments based on predicted gene transcripts from the Ensembl project. One can search for transcripts via keyword, or do a batch search by providing a list of Ensembl identifiers.
http://oligodb.charite.de/

OligoCalc - (Found June 29, 2008 )

OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5 and 3 chemical modifications and predict potential hairpin loop formation.
http://www.basic.northwestern.edu/biotools/OligoCalc.html

NTMG - (Found June 29, 2008 )

NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
http://oblab.cs.nchu.edu.tw:8080/WebSDL/

NEBcutter - (Found June 29, 2008 )

NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
http://tools.neb.com/NEBcutter/index.php3

MutScreener - (Found June 29, 2008 )

MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.
http://bioinfo.bsd.uchicago.edu/MutScreener.html

MuPlex - (Found June 29, 2008 )

Multi-Objective Multiplex PCR Assay Design (MuPlex) is a tool to assist in the design of multiplex PCR assays. MuPlex takes a set of DNA sequences and other experimental information as input and provides a set of multiplex PCR assays intended to cover as many of the user-supplied sequences as possible.
http://genomics14.bu.edu:8080/MuPlex/MuPlex.html

LNAtools - (Found June 29, 2008 )

LNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, real time PCR, and SNP genotyping.
http://lnatools.com/