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QUMA

http://quma.cdb.riken.jp/

Description :
Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. Users can also control the quality of aligned sequences by changing cutoff paramteres.

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeR

http://guinevere.otago.ac.nz/stats.html

Description :
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. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.

IDT SciTools

http://www.idtdna.com/SciTools/SciTools.aspx

Description :
IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.

OligoHeatMap

http://bioinfo.unice.fr/ohm/

Description :
OligoHeatMap is an online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically.

DNA Learning Center, Cold Spring Harbor Laboratory

http://www.dnalc.org/ddnalc/websites/

Description :
excellent online genetics activities, including BioServers bioinformatics tools designed for teachers and students, and animations explaining techniques such as PCR.

SNPbox

http://www.snpbox.org/

Description :
Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.

SNP Cutter

http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

Description :
SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.

MuPlex

http://genomics14.bu.edu:8080/MuPlex/MuPlex.html

Description :
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.

Assembly PCR Oligo Maker

http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html

Description :
Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.

CODEHOP

http://blocks.fhcrc.org/codehop.html

Description :
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.

Electronic PCR

http://www.ncbi.nlm.nih.gov/sutils/e-pcr

Description :
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.

Gene2Oligo

http://berry.engin.umich.edu/gene2oligo/

Description :
Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).

Genefisher

http://bibiserv.techfak.uni-bielefeld.de/genefisher/

Description :
Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.

GLUE, PEDEL, and DRIVeR

http://guinevere.otago.ac.nz/mlrgd/STATS/index.html 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.

NTMG

http://oblab.cs.nchu.edu.tw:8080/WebSDL/

Description :
NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.

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