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A comparative account of primer designing resources, feature-validations and application-based categorizations : Microarray probes
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Array Designer
http://www.premierbiosoft.com/dnamicroarray/index.html
Allows the user to input multiple targets and designs probes for gene expression profiling and SNP detection.
Not available
Not available
100
Features are written as claimed by the author. Not validated completely.
CommOligo
http://ieg.ou.edu/software.htm
1. Selects optimal oligonucleotides for microarray construction. 2. Flexible for the user to choose values for different parameters, such as sequence identity, the length of maximum continuous stretches, and free energy. The length of oligonucleotide can be from 8 to 128mer.
Li X, He Z, Zhou J. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res. 2005 Oct 24;33(19):6114-23. Print 2005. PubMed PMID: 16246912.
2005
100
Features are written as claimed by the author. Not validated completely.
CommOligo2.0
http://ieg.ou.edu/software.htm
1. This software is developed based on CommOligo. 2. Designs probes for a group of highly homologous sequences.
Not available
Not available
100
Features are written as claimed by the author. Not validated completely.
Mprime
http://kbrin.a-bldg.louisville.edu/Tools/MPrime/
1. Designs multiple primers for genes in human, rat, mouse, drosophila, and zebra fish. 2. Allows the user to select one or more inputs provided by the user to design primers for a single or multiple targets.
Rouchka EC, Khalyfa A, Cooper NG. MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics. 2005 Jul 13;6:175. PubMed PMID: 16014168.
2005
100
Oligo Design
http://www.enme.umd.edu/bioengineering/
Designs primers for detection and identification of bacteria based on known short sequence of DNA.
Herold KE, Rasooly A. Oligo Design: a computer program for development of probes for oligonucleotide microarrays. Biotechniques. 2003 Dec;35(6):1216-21. PubMed PMID: 14682056.
2003
100
Features are written as claimed by the author. Not validated completely.
OligoFaktory
http://www.bioinformatics.org/oligofaktory/
Schretter C, Milinkovitch MC. OligoFaktory: a visual tool for interactive oligonucleotide design. Bioinformatics. 2006 Jan 1;22(1):115-6. Epub 2005 Oct 20. PubMed PMID: 16239305.
2006
100
Not yet identified the unique feature of the tool. Features are written as claimed by the author. Refer "Feature Table" for the detail description of the tool.
Osprey
http://osprey.ucalgary.ca
1. Designs PCR and microarray primers. 2. Also involves in oligo analysis
Gordon PM, Sensen CW. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res. 2004 Sep 29;32(17):e133. PubMed PMID: 15456895.
2004
100
Did not give results when tested [as per the 5th july, 2011].
PrimeArray
christoph.dehio@unibas.ch
Raddatz G, Dehio M, Meyer TF, Dehio C. PrimeArray: genome-scale primer design for DNA-microarray construction. Bioinformatics. 2001 Jan;17(1):98-9. PubMed PMID: 11222267.
2001
100
To access the tool, need to get permission from the author. So not yet validated the tool, but general features are written as claimed by the author. See "Feature Table" for the description of the tool.
UniFrag
http://bioinformatics.biol.rug.nl/websoftware/unifrag/unifrag_start.php
van Hijum SA, de Jong A, Buist G, Kok J, Kuipers OP. UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinformatics. 2003 Aug 12;19(12):1580-2. PubMed PMID: 12912842.
2003
100
Not yet identified the unique feature of the tool. Features are written as claimed by the author. Refer "Feature Table" for the detail description of the tool.
RTPrimerdb
http://www.rtprimerdb.org/
1. It is a database that holds primers and probes used for real time PCR assay. 2. There are 8606 real time PCR assays detailing 5928 genes.
Steve Lefever, Jo Vandesompele, Frank Speleman and Filip Pattyn: RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Research. 2008 Oct 8;37(1):D942-D945. PubMed PMID: 18948285; PubMed Central PMCID: PMC2686610
2009
100
There are two older version of this database. One is 2003 version and other is 2006 version
 
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