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A comparative account of primer designing resources, feature-validations and application-based categorizations : Phylogenetic analysis
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Primaclade
http://dousta.umsl.edu/cgi-bin/primaclade.cgi
Conserved primer designing.
Gadberry MD, Malcomber ST, Doust AN, Kellogg EA. Primaclade--a flexible tool to find conserved PCR primers across multiple species. Bioinformatics. 2005 Apr 1;21(7):1263-4. Epub 2004 Nov 11. PubMed PMID: 15539448.
2005
100
Unable to use the vector of my choice as claimed by the author.
Primers4clades
http://maya.ccg.unam.mx/primers4clades/ http://floresta.eead.csic.es/primers4clades/
1. Designs PCR primers for cross-species amplification of novel sequences from metagenomic DNA and from uncharacterized organisms belonging to user defined phylogenetic clades or taxa. 2. Useful for phylogenetic analysis.
Contreras-Moreira B, Sachman-Ruiz B, Figueroa-Palacios I, Vinuesa P. primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W95-W100. Epub 2009 May 21. PubMed PMID: 19465390.
2009
100
Features are written as claimed by the author. Not validated completely.
Primique
http://cgi-www.cs.au.dk/cgi-chili/primique/front.py
Designs primer pairs specific to the family of closely related species.
Fredslund J, Lange M. Primique: automatic design of specific PCR primers for each sequence in a family. BMC Bioinformatics. 2007 Oct 3;8:369. PubMed PMID: 17910777; PubMed Central PMCID: PMC2045118.
2007
100
Primrose
http://www.bioinformatics-toolkit.org/Primrose/index.html
Not available
Not available
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.
SeqState
http://bioinfweb.info/Software/SeqState
Müller K. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Appl Bioinformatics. 2005;4(1):65-9. PubMed PMID: 16000015.
2005
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.
 
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