Questions tagged [primer]
Short sequence of DNA which hybridises to a locus within a genome and is used to initate replication of a unit of DNA through the DNA polymerase enzyme. Essential for PCR
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Aligning sequence and comparing it against primer
I am looking to show how a primer is consistent among some genomic data. I have a primer of about 23bp and looking to compare it to about 5000 genomic sequences of 10kb. I am unsure how to format it ...
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programmatic secondary structure prediction for >36-mer DNA oligonucleotides
I'm writing a tool to automate Sanger sequencing primer design for a production lab that uses a universal-tail chemistry Sanger sequencing to verify NGS results. Essentially, the template DNA is ...
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What is a poly(T) primer anchor sequence?
I am reading Tang et al. (2009).
In the method description it is stated that:
A single cell is manually picked under a microscope and lysed. Then mRNAs are reverse-transcribed into cDNAs using a ...
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Hard-clip primers in a bam file
I am working on a sample which was sequenced using an amplicon kit and I would like to ensure that no variants are called in the PCR primer sequences. I know that the primer sequences are part of the ...
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Which non-matching DNA bases clash the least?
I am building primers for LAMP which I know will not match all my target sequences perfectly.
To some extent, having primers with multiple variants at variable sites (degenerate primers) and longer ...
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What is the "primer masterfile" format?
I am working with an amplicon kit from Swift Bioscience and they provide the primer locations in what they call a "masterfile". The format is like this:
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Hits in Primer-BLAST not found with programmatic blastn query
Summary:
I'm writing an automated tool for designing Sanger sequencing primers (other tools don't do exactly what I want) that will be incorporated in a production diagnostic laboratory for on-demand ...
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Can Primer-BLAST be run locally?
Primer-BLAST is a tool for designing target-specific primers, available through the Primer-BLAST web interface.
Is it possible to run the tool locally instead of accessing it via the internet?
Primer-...
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Primer trimming-fasta files
My goal:
I want to trim off the primers (Forward : CGAGAAGACCCTRTGRAGCT, Reverse : GTTGGGGYGACCNYGG) from a fasta file with a lot of dna sequences allowing for some (e.g. 3) mismatches (identity).
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Do you know a program/script to count how many sequences have mismatches on each position of my primers?
I'm working with primer analysis and design, and so far I've performing it in Excel but: a) I don't like Excel, b) I do it manually, c) I don't like Excel, d) it gets tedious when working with ...
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Primer-Blast Custom Database [error]
I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality.
However whenever I try to upload a FASTA file as ...
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Which software is recommended for sequencing primers selection?
I have a list of primers for sequencing fungal ITS1/2 regions. I also have access to different fungal databases. I would like to perform in silico PCR analysis for comparing different primer pairs and ...
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LAMP primers design software
What software do you use to design LAMP reaction primers for alignment? So far I have been using Primer Explorer v5 but I am looking for some alternatives.
Alignment includes some species from the ...
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How likely is it to find primers sequences in already-trimmed reads?
So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition.
After removing primers (using cutadapt) from both R1 ...
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Can you give me a detailed explanation about PrimeBlast?
I am trying to write a research paper on PRIMER-BLAST. I have read something about it on
https://www.ncbi.nlm.nih.gov/pubmed/22708584/
but still, it is not enough. So can you please tell me more ...
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