How do you cite NCBI primer-blast?
How do you cite NCBI primer-blast?
Resource Report
- URL: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
- Proper Citation: Primer-BLAST (RRID:SCR_003095)
- Description: A tool to design target-specific primers for polymerase chain reaction (PCR).
How do you cite a primer?
How to cite “Primer” (movie)
- APA. Carruth, S. (2004). Primer. THINKFilm.
- Chicago. Carruth, Shane. 2004. Primer. United States: THINKFilm.
- MLA. Carruth, Shane. Primer. THINKFilm, 2004.
Where can I find primer binding site?
You will start to get sequence ~20 bp downstream of your primer. If the PCR product is <800 bp then your sequence should run toward the opposing primer and will end around 5-10 bp from the end of your PCR product. From here you should be able to get an approximation of the primer binding site in your target gene.
How do you design forward and reverse primers for PCR?
Forward and reverse primers should be about 500 bp apart. The 3′ end of the primer should be a G or a C. The genomic sequence that comes from the computer is just one strand; the complementary strand is not shown. For the forward primer, you can use the sequence directly.
How do you choose primers for PCR?
PCR Primer Design Tips
- Aim for the GC content to be between 40 and 60% with the 3′ of a primer ending in G or C to promote binding.
- A good length for PCR primers is generally around 18-30 bases.
- Try to make the melting temperature (Tm) of the primers between 65°C and 75°C, and within 5°C of each other.
How do you cite a blast result?
For the command-line version of NCBI BLAST, and for details of the BLAST method, you would cite:
- Camacho C. et al.
- Altschul S.F. et al. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”
- Altschul S.F. et al. (1990) “Basic local alignment search tool”
How do you cite PrimerBank?
You can cite the following papers describing the work done for the PrimerBank database. PrimerBank IDs should also accompany the cited primer pairs. Athanasia Spandidos, Xiaowei Wang, Huajun Wang and Brian Seed: PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.
How do you validate primers?
Validating Primer Design
- Primers are homologous to the desired target sequence.
- Appropriate splice variants are detected.
- SNPs have been avoided unless required for the assay.
- The oligos and amplicon do not adopt a secondary structure.
- There is low potential for the oligos of the reaction to hybridize to each other.
What is the Primer-BLAST tool?
This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers.
How do I find citations/papers for NCBI services?
Use the Citation link on the right side of the PMC view of this article to obtain the citation in the desired format. Check through this PubMed listing to locate citations/papers on individual NCBI services of your interest. For the BLAST® services, use these BLAST references.
How do I reference the blast® services?
For the BLAST® services, use these BLAST references. 2. Citing the NCBI internet site and individual web pages and records: National Center for Biotechnology Information (NCBI) [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2017 Apr 06].
Can Primer-BLAST determine if a database sequence is an intended target?
However, in some cases, primer-blast cannot determine if a database sequence is an intended target or not, thus the user guidance might be helpful (For example, when your template is a polymorphic form or a partial region of an entry in the search database, or when the database such as the nr contains redundant entries of your template).
