Scrimer: designing primers from transcriptome data
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F15%3A10314408" target="_blank" >RIV/00216208:11310/15:10314408 - isvavai.cz</a>
Alternative codes found
RIV/68081766:_____/15:00443615 RIV/68378050:_____/15:00443615
Result on the web
<a href="http://dx.doi.org/10.1111/1755-0998.12403" target="_blank" >http://dx.doi.org/10.1111/1755-0998.12403</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/1755-0998.12403" target="_blank" >10.1111/1755-0998.12403</a>
Alternative languages
Result language
angličtina
Original language name
Scrimer: designing primers from transcriptome data
Original language description
With the rise of next-generation sequencing methods, it has become increasingly possible to obtain genomewide sequence data even for nonmodel species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which cansubsequently be screened in a larger population sample using a variety of genotyping techniques. Many of these techniques require appropriate locus-specific PCR and genotyping primers. Currently, there is no publicly available software for the automateddesign of suitable PCR and genotyping primers from next-generation sequence data. Here we present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash workflow that conne
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
EB - Genetics and molecular biology
OECD FORD branch
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Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Molecular Ecology Resources
ISSN
1755-098X
e-ISSN
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Volume of the periodical
15
Issue of the periodical within the volume
6
Country of publishing house
GB - UNITED KINGDOM
Number of pages
6
Pages from-to
1415-1420
UT code for WoS article
000362838300015
EID of the result in the Scopus database
2-s2.0-84943553772