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.

SSR Primer - (Found June 29, 2008 )

Simple Sequence Repeats (SSR) Primer aids in design of primers that can amplify microsatellite sequences. SPUTNIK is used to screen for SSR and Primer3 for locus specific primer design. Precomputed results can be viewed using the SSR Taxonomy Browser.
http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html

SOP3v2 - (Found June 29, 2008 )

SOP3v2 takes a list of gene names, a list of reference sequence IDs or a chromosomal location as input and provides a set of PCR and sequencing primers as output. These primers are optimized for sequence-based genotyping assays.
http://imgen.ccbb.pitt.edu/sop3v2/

Sockeye - (Found June 29, 2008 )

Sockeye is a visualization tool allowing one to assemble and analyze genomic information in a three dimensional workspace. It can be used to view features at various levels, ranging from SNPs to karyotypes. Sockeye displays genomic features along tracks, and links to the Ensembl database.
http://www.bcgsc.ca/gc/bomge/sockeye/

SNPmasker - (Found June 29, 2008 )

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.
http://bioinfo.ebc.ee/snpmasker/

SNPbox - (Found June 29, 2008 )

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.
http://www.snpbox.org

Primaclade - (Found June 29, 2008 )

Primaclade accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers that will bind across the alignment.
http://dousta.umsl.edu/cgi-bin/primaclade.cgi

PriFi - (Found June 29, 2008 )

PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs.
http://cgi-www.daimi.au.dk/cgi-chili/PriFi/main

Gene2Oligo - (Found June 29, 2008 )

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

Electronic PCR - (Found June 29, 2008 )

Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
http://www.ncbi.nlm.nih.gov/sutils/e-pcr

E-RNAi - (Found June 29, 2008 )

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in Drosophila and C. elegans; can also be used for the design of enzymatically-digested long dsRNA (esiRNAs) for mammalian cells.
http://e-rnai.dkfz.de/