| Array Designerhttp://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.
Features are written as claimed by the author. Not validated completely. |
| CommOligohttp://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.
Features are written as claimed by the author. Not validated completely. |
| CommOligo2.0http://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.
Features are written as claimed by the author. Not validated completely. |
| Mprimehttp://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 Designhttp://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.
Features are written as claimed by the author. Not validated completely. |
| OligoFaktoryhttp://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.
"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." |
| Ospreyhttp://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].
Did not give results when tested [as per the 5th july, 2011]. |
| PrimeArraychristoph.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.
"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." |
| UniFraghttp://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.
"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." |
| RTPrimerdbhttp://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
There are two older version of this database. One is 2003 version and other is 2006 version |
