arrow

From NeuroLex

Jump to: navigation, search



Resource:PrimerStudio

Name: Resource:PrimerStudio
Description:

"PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome.
Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs.
-There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names)
-you can use genome regions (chromosome coordinates, chromosome bands if exists)
-Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers
-euPCR for eukaryotic organisms genes/exons primers
-snpPCR for eukaryotic organisms SNP primers

Sponsors: PrimerStudio is funded by the University of Tartu.
Other Name(s): PrimerStudio
Resource Type(s): Database
Resource: Resource
URL: http://bioinfo.ebc.ee/PrimerStudio/
Id: nif-0000-21334
Keywords: eukaryotic, exon, gene, amplicon, amplifcation, analysis, dinucleotide, dna, genome, genomic, molecular probe and primer databases, mononucleotide, mutation, organism, pcr, primer, prokaryotic, region, repetitive, segment, sequence, snp, snp detection
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

This resource will be curated within 7 days.

For Resource Owners:
After the resource is curated, you may create a sitemap, which will help keep your registry description up-to-date and inform search engines about your resource.

Note: For a new resource, the website's URL must first be verified by a NIF curator before you may proceed.

Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site. Please login to create the sitemap. (top right)

This page uses this default form:Resource

Contributors

Ccdbuser, Nifbot2, Zaidaziz



bookmark
Facts about Resource:PrimerStudioRDF feed
CurationStatusuncurated  +
DefiningCitationhttp://bioinfo.ebc.ee/PrimerStudio/  +
Definition

"PrimerParadise is an online PCR p
"PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome.
Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs.
-There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names)
-you can use genome regions (chromosome coordinates, chromosome bands if exists)
-Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers
-euPCR for eukaryotic organisms genes/exons primers
-snpPCR for eukaryotic organisms SNP primers

Sponsors: PrimerStudio is funded by the University of Tartu.
s funded by the University of Tartu.
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-21334  +
KeywordsEukaryotic  +, Exon  +, Gene  +, Amplicon  +, Amplifcation  +, Analysis  +, Dinucleotide  +, Dna  +, Genome  +, Genomic  +, Molecular probe and primer databases  +, Mononucleotide  +, Mutation  +, Organism  +, Pcr  +, Primer  +, Prokaryotic  +, Region  +, Repetitive  +, Segment  +, Sequence  +, Snp  +, and Snp detection  +
LabelResource:PrimerStudio  +
ModifiedDate17 June 2013  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymPrimerStudio  +