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.

WebTraceMiner - (Found June 29, 2008 )

WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3' and 5' termini of cDNA inserts by detecting sequence features such as vector fragments, adapterlinker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.
http://www.conifergdb.org/software/wtm1.0/

siRNA Selection Server - (Found June 29, 2008 )

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA.
http://jura.wi.mit.edu/bioc/siRNA

siDirect - (Found June 29, 2008 )

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.
http://design.rnai.jp/

Sfold - (Found June 29, 2008 )

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.
http://sfold.wadsworth.org

REPK - (Found June 29, 2008 )

REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.
http://rocaplab.ocean.washington.edu/tools/repk

REBASE - (Found June 29, 2008 )

The Restriction Enzyme Database, a collection of information about restriction enzymes and related proteins.
http://rebase.neb.com/rebase/rebase.html

QPPD - (Found June 29, 2008 )

QPPD (Quantitative PCR Primer Database) contains information about primer sets published for quantitative PCR assays. This database can be searched by gene name, keyword, or by identifier. Results return primer sequences, graphics showing the primer location, and PubMed ID for the original reference.
http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp

PUNS: Primer-UniGene Selectivity Testing - (Found June 29, 2008 )

The Primer-UniGene Selectivity Testing software system (PUNS) assists in the specificity design of PCR primers. A set of primers must be physically designed first. Then PUNS can be used to estimate the expected number of different amplification products using NCBI's UniGene database as representative of species transcriptomes.
http://okeylabimac.med.utoronto.ca/PUNS/

ProbeLynx - (Found June 29, 2008 )

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.
http://www.pathogenomics.ca/probelynx

Primer3Plus - (Found June 29, 2008 )

Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi