| Some softwares for oligonucleotides design | |||
| softwares | Articles | Comments | URL |
| probemaker | ProbeMaker: an extensible framework for design of sets of oligonucleotide probes (PMID: 16171527) | some bugs with linux (mandriva 2007) | http://probemaker.sourceforge.net/ |
| OligoArray 2.1 | OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach (PMID: 12799432) | for genomic. - methods Tm, mfold, blast for specificityC8 | http://berry.engin.umich.edu/oligoarray/ |
| Gene2oligo | Gene2Oligo: oligonucleotide design for in vitro gene synthesis (PMID: 15215375) | for genomic | http://berry.engin.umich.edu/gene2oligo/ |
| ? | Application of a unique server-based oligonucleotide probe selection tool toward a novel biosensor for the detection of Streptococcus pyogenes (PMID: 17011180) | - single sequence - specifcity by blast - written in VB. Can not download | |
| Primegens | PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. (PMID: 12424113) | oligonucleodites for genomic arrays | http://compbio.ornl.gov/structure/primegens/ |
| Osprey | Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays (PMID: 15456895) | not tested | http://osprey.ucalgary.ca/ |
| ARB project | ARB: a software environment for sequence data (PMID: 14985472) | - package with many tools - ARB probe library :database for bacteria probes (16s) with a phylogenic tree | http://www.arb-home.de/ |
| PROBEmer | PROBEmer: A web-based software tool for selecting optimal DNA oligos. (PMID: 12824409) | - set of targets and set of non-targets (% of sequences in each group.) some tests with 16S in article -not tested because unavailable web site for download | http://probemer.cs.loyola.edu |
| GeneFisher | GeneFisher--software support for the detection of postulated genes. (PMID: 8877506) | (calculate a consensus with target-sequences) - online version (in ajax - consensus with target sequences - can not use a non-target set of sequences - difficulty to choose options in order to get probes | http://bibiserv.techfak.uni-bielefeld.de/genefisher2/ |
| CommOligo | Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation | - Allow to use a set of sequences - Check specifity with a set of non-target sequences by using a blast like methode (better) - For windows users only - Seems to be nice but unable to get this software (unable to contact authors) | ? |
| Oligopicker | Selection of Oligonucleotide Probes for Protein Coding Sequences (PMID: 12724288) | rather for genomic studies problem with some non-numeric ID (in fasta files) | http://pga.mgh.harvard.edu/oligopicker/ |
| primer clade | Primaclade: a web-based program for designing primers from multiple alignments | - design of primers in a set of target sequences (consensus) and with aligned sequences (clustalw used). - Use of primers3 in background - online tool (rather easy and fast) | http://dousta.umsl.edu/cgi-bin/primaclade.cgi |
| AlleleID | AlleleID: a pathogen detection and identification system (pmid :17951804) | - Very comprehensive (but not easy to use) - For identification of species - targets set , non-targets set, etc... - commercial software | http://www.premierbiosoft.com |
| Yoda | YODA: Yet-another Oligonucleotide Design Application (PMID: 15572465) | - accepts targets and non-targets sequences - Seems to be simple and efficient. Some problems with my linux. | http://pathport.vbi.vt.edu/YODA |
| OligoSpawn | OligoSpawn: a software tool for the design of overgo probes from large unigene datasets (PMID: 16401345) | works with unigene. - Set of targets and set of non-targets - not tested | http://oligospawn.ucr.edu/. |
| hyther | - Design of primers with different modules - Single target sequence | http://ozone3.chem.wayne.edu/ | |
| Visual OMP 3 | Physical principles and visual-OMP software for optimal PCR design. (PMID: 17951788) | - like hyther - commercial | http://www.dnasoftware.com/Products/VisualOMP/ |
| sarani | Automatic design of primers for genonic studies commercial | ||
| Array Designer 2 | |||
| Primer pro 3.4 Primer unique | - design primers. Check in non-target sequences. - commercial. Some gaps | http://www.changbioscience.com/primo/primo.html | |
| Primer Premier v5 | commercial. hard to use quickly | http://www.bio.com/ | |
| Array Designer 2 Beacon Designer 7 Xpression Primer | commercial | http://www.bio.com/ | |
| oligo 6 | - use of a set of target sequences (consensus) - commercial (win + mac only) | http://www.philscience.com/oligo/p1.htm | |
| oligowiz ProbeWiz server | - multi target sequences ? - some problems with linux - article with primers design softwares comparisons ProbeWiz server = like oligowiz but online | http://www.cbs.dtu.dk/services/OligoWiz2/ | |
| netprimer | ? | not tested (command line) | |
| perlprimer | ? | not tested (command line) | |
| primerbase | - database of primers - not update – unavailable | ||
| autoprime | expression arrays (use ensembl) | ||
| primer3 | single target sequence | http://frodo.wi.mit.edu/ | |
| arrayoligoselector | primers for genomes | ||
| oligoDB | for transcriptome | ||
| Featurama – probepicker | not tested (command line) | http://probepicker.sourceforge.net/ | |
| Roso | ROSO: optimizing oligonucleotide probes for microarrays (PMID: 14734320) | expression arrays | |
| OligoArray 2.1 | - single sequence input - commercial - many options | http://www.philscience.com/oligo/index.htm | |
| Some articles | |||
| Detection of bacterial pathogens in environmental samples using DNA microarrays (PMID: 12654494 ) | |||
| Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. (PMID: 16461729) | |||
| Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation (PMID: 16246912) | |||
| Empirical establishment of oligonucleotide probe design criteria. (PMID: 16000786) | |||
| Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays (PMID: 11071945) | |||
| Automated Detection and Quantitation of Bacterial RNA by Using Electrical Microarrays (PMID: 16841897) | |||
| Microarrays for bacterial detection and microbial community analysis (PMID: 12831906) | |||
| Web sites | |||
| http://www.humgen.nl/primer_design.html (liste logiciels pour design d'amorces) | |||