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PRIMEX specifications

Information


Unique identifier OMICS_15793
Name PRIMEX
Alternative name PRImer Match Extractor
Interface Web user interface
Restrictions to use None
Input data For a query remote, an oligonucleotide 13-40 bases long (ACCGTCTAGCTAGCT) is needed. For get a sequence remote, two numbers separated by a colon (12500:12550) are needed.
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_15793
Name PRIMEX
Alternative name PRImer Match Extractor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.1
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for PRImer Match Extractor

PRIMEX citations

 (3)
library_books

Improved assay dependent searching of nucleic acid sequence databases

2008
Nucleic Acids Res
PMCID: 2475610
PMID: 18515842
DOI: 10.1093/nar/gkn301

[…] ion for sampling in the presence of a complex background) and sensitivity of the search algorithm. Many existing tools can search a database with a pair of PCR primers, including e-PCR (), me-PCR (), PRIMEX (), simPCR (), BiSearch (), SPCR () and iPCRess (). However, none of these programs support additional assay formats (e.g. TaqMan™ PCR, an assay commonly used for pathogen detection). Additiona […]

library_books

GENOMEMASKER package for designing unique genomic PCR primers

2006
BMC Bioinformatics
PMCID: 1450303
PMID: 16566824
DOI: 10.1186/1471-2105-7-172

[…] s against genomic DNA []. These methods are relatively fast, but unfortunately all of them require specific parsers to count all primer binding sites and to find all PCR products on the template DNA. PRIMEX [], on the other hand is specifically designed for testing oligos and counting primer binding sites from genomic DNA. Another recently reported program, me-PCR [], is designed for the detection […]

library_books

Information theory based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

2005
BMC Bioinformatics
PMCID: 1183192
PMID: 16042814
DOI: 10.1186/1471-2105-6-190

[…] field, such as longest common factor approach proposed by Rahmann [], hybridization free energy based method used by Li [], Kaderali's work [] based on an extended nearest neighbor model, and Lexa's PRIMEX [].In our research, we designed a new algorithm based on information theory. One information source was obtained by converting the primer sequences to numeric vectors of the potential full hydr […]

Citations

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PRIMEX institution(s)
Laboratory of Functional Genomics and Proteomics, Masaryk University Brno, Brno, Czech Republic; CRIBI Biotechnology Center, University of Padova, Padova, Italy

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