Restriction Map
Primers
Local programs on dapsas/inn
GCG programs - available from SeqWeb on dapsas
or on inn
- Prime- selects oligonucleotide primers for a template DNA sequence
- PrimePair - evaluates individual primers to determine their compatibility
- MeltTemp - computes the melting temperature of oligonucleotides
EMBOSS programs - available on inn
or on dapsas
- EPRIMER3 - Picks PCR primers and hybridization oligos
- PRIMERSEARCH - Searches DNA sequences for matches with primer pairs
- STSSEARCH - Searches a DNA database for matches with a set of STS primers
Remote programs:
primer-blast at NCBI
PRIMO 3.4: A suite of primer design programs, including: Regular, Degenerate (based on single sequence or multiple alignment), Unique (in case of closely related sequences, can find unique primers), Site Directed mutagenesis, inverse, multiplex and many more
PRIMO: A primer design tool (Kupfer, Li)
ASepcr Alternative Splicing electronic RT-PCR in multiple tissues and organs
The Primer Generator finds primers for site directed mutagenesis
Primer3 a web server for primer design
PRIMER3 - downloadable sourcecode for primer3
, and Primer3 a friendlier but older version.
Primer selection - at BCM
NetPrimer
Web-Primer - PCR design program for yeast (SGD - Saccharomyces Genome Database
CloneIt finding sub-cloning strategies
CODEHOP
- COnsensus-DEgenerate Hybrid Oligonucleotide Primers at the USA BLOCKS server
InSilico PCR
Restriction Map
Local programs on dapsas/inn
GCG programs - available from SeqWeb on dapsas or on inn
- map - displays restriction sites and protein translations
- mapsort - finds the coordinates of the restriction enzyme cuts in a DNA sequence
- mapplot - displays restriction sites graphically
EMBOSS programs - available on inn
or on dapsas
- RESTOVER - Finds restriction enzymes that produce a specific overhang
- REMAP - Display a sequence with restriction cut sites,translation etc..
- RESTRICT - Finds restriction enzyme cleavage sites
- SILENT - Silent mutation restriction enzyme scan
- REDATA - Search REBASE for enzyme name, references, suppliers etc
- RECODER - Remove restriction sites but maintain the same translation
Remote programs: