||Task ||Name ||Licence ||Packaging || ||Importance ||
||Primer design ||[[http://www.egs.uu.se/software/tagenerator/|TagGenerator]] ||GPL ||depends on BioPerl and ncbi-blast || ||free ||
||In Silico PCR ||[[http://www.ebi.ac.uk/~guy/exonerate/ipcress.man.1.html|ipcress]] ||LGPL ||part of the [[http://www.ebi.ac.uk/~guy/exonerate/debian/|exonerate]] package || ||free ||
||Primer design and in silico PCR ||[[http://arep.med.harvard.edu/kzhang/polHap/PrimerDesign.html|yamPCR]] ||no licence ||Depends on bioperl, blast2, primer3 (to be patched) || ||sounds powerful... and power-hungry ||
||<style="vertical-align: top;">Primer Design across exon-intron junctions, uses Primer3 and BLAT ||<style="vertical-align: top;">!ExonPrimer ||<style="vertical-align: top;">no licence ||<style="vertical-align: top;">Webpage Javascript ||<style="vertical-align: top;"> ||<style="vertical-align: top;">Free ||
||<style="vertical-align: top;">Oligo Properties Calculator for TaqMan and SYBR Green oligos ||<style="vertical-align: top;">[javascript:void(0);/*1232001073765*/ Beacon Designer (Free Edition)] ||<style="vertical-align: top;">no licence ||<style="vertical-align: top;">Webpage Javascript ||<style="vertical-align: top;"> ||<style="vertical-align: top;">Free ||
||Primer design ||[[http://www.genome.ou.edu/informatics/primou.html|primou]] ||not found || || || ||
||Oligonucleotide analysis ||[[http://www.basic.northwestern.edu/biotools/oligocalc.html|Oligonucleotide properties calculator]] ||free distribution for education and non-commercial ||javascript web page || ||available on the web anyway ||
||Oligonucleotide analysis ||[[http://probemaker.sourceforge.net/|probemaker]] ||GPL ||java || ||free ||
||Synthethic gene design ||[[http://slam.bs.jhmi.edu/gd/|GeneDesign]] ||none? ||perl CGI || || ||
||Analysis of bisulphite PCR results ||[[http://biq-analyzer.bioinf.mpi-inf.mpg.de/|BiQ Analyzer]] ||[[http://biq-analyzer.bioinf.mpi-inf.mpg.de/License_Agreement.txt|redistribution is forbiden]] ||disallowed || ||no packaging ||
||Normalisation of qPCR ||[[http://www.mdl.dk/publicationsnormfinder.htm|Normfinder]] ||Not found ||R script || || ||
||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||<style="vertical-align: top;"> ||
||RNA secondary structure visualization ||jViz.Rna ||GPL (to clarify) ||java || ||seems useful ||
||Molecular structure visualisation ||QuteMol ||[[http://sourceforge.net/projects/qutemol|GPL]] ||free || ||not important ||
||Epitope mapping ||[[http://pepitope.tau.ac.il/sources.html|PepSurf]] ||not found ||looks easy || || ||
||Task ||Name ||Licence ||Packaging || ||Importance ||
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