Mapping and Primers Analysis
- Primers
- Restriction Map
Primers
Local programs available on sura
- EMBOSS programs - available on open in new windowweb or on command line on sura
- 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
- open in new windowprimer-blast at NCBI
- open in new windowPrimer3web at MIT for primer design
- open in new windowPrimer3Plus with additional sequencing options
- open in new windowPRIMO 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
- open in new windowPRIMO: A primer design tool (Kupfer, Li)
- open in new windowASepcr Alternative Splicing electronic RT-PCR in multiple tissues and organs
- open in new windowPRIMER3 - downloadable sourcecode for primer3, and Primer3 a friendlier but older version.
- open in new windowNetPrimer
- open in new windowWeb-Primer - PCR design program for yeast (SGD - Saccharomyces Genome Database
- open in new windowPrimaclade - program to design degenerate primers
- open in new windowHyden - a downloadable program for degenerate primers
- open in new windowOligocalc - Oligonucleotide Properties Calculator
- open in new windowInSilico PCR simulation of molecular biology experiments
Remote programs:
- EMBOSS programs - available on open in new windowweb or on command line on sura
Restriction Map
Local programs on dapsas
- EMBOSS programs - open in new windowweb or on command line on sura
- 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
- open in new windowWebCutter 2
- open in new windowWatCut An on-line tool for restriction analysis, silent mutation scanning, and SNP-RFLP analysis
- open in new windowSeqCUTTER
- open in new windowTACG restriction enzyme analysis and mapping
- open in new windowRestrictionMapper
- open in new windowNetPlasmid Online Plasid Map drawing
- open in new windowNEBCUtter finds the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once