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Primaclade | A flexible tool to find conserved PCR primers across multiple species

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Designs minimally degenerate primers for comparative studies of multiple species. Primaclade is a web-based primer prediction application that provides a solution for researchers who want to design Polymerase Chain Reaction (PCR) primers across multiple species. The software generally performed best with alignments of up to about eight sequences and up to 29.0% sequence divergence. It can simplify the design of PCR primers for any comparative molecular study.

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Primaclade classification

Primaclade specifications

Unique identifier:
OMICS_02356
Restrictions to use:
None
Output data:
A page containing the original alignment file displayed horizontally across the top of the page, followed by a single line showing the consensus sequence, the list of generated primers corresponding to their correct position within the alignment display and reverse complement for the 3' primers.
Computer skills:
Basic
Maintained:
Yes
Interface:
Web user interface
Input format:
FASTA, clustalw, PHYLIP, nexus, mega, emboss
Output format:
HTML
Stability:
Stable

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Primaclade forum

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Primaclade classification

Primaclade specifications

Unique identifier:
OMICS_02356
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
Comprehensive Perl Archive Network (CPAN) Perl modules, BioPerl modules, the Primer3 software
Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Perl
Stability:
Stable

Primaclade distribution

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Primaclade support

Maintainer

  • Elizabeth A. Kellogg <>
This tool is not maintained anymore.

Credits

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Publications

Institution(s)

Department of Biology, University of Missouri-St Louis, One University Boulevard, St Louis, MO, USA

Funding source(s)

Supported by NSF grants MCB-0110809 and DBI-0110189.

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