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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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PCR primers for detecting hetero vs homozygous and WT mice in our colony

My PI has asked me for advice on making a PCR screen to identify mice from a particular Cre line. We have multiple Cre lines in the colony so it can't just be for mice with a copy of Cre in their ...
Angus Campbell's user avatar
3 votes
1 answer
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1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?

I would like to know the steps of this question and how to determine the forward and the reverse primers and also the length of the sequence, without using NCBI. If you could explain and give an ...
Teo's user avatar
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Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q

Could you help me bioinformatics SE people. So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
RPINerd's user avatar
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Do we design primers for single stranded DNA with same criteria as we do for double stranded DNA?

I am trying to design primers for a single stranded DNA virus. But I am having a dilemma as whether we design the primers same way as double stranded DNA? do we have to design forward and reverse ...
Maharshi's user avatar
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2 votes
1 answer
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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 ...
Laura's user avatar
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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 ...
pourpre's user avatar
1 vote
1 answer
301 views

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). ...
Damianos's user avatar
2 votes
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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-...
Tony's user avatar
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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 ...
gabt's user avatar
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1 vote
1 answer
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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 ...
Gaston's user avatar
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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 ...
Pranav Choudhary's user avatar
1 vote
2 answers
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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 ...
Set's user avatar
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2 votes
2 answers
410 views

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 ...
terdon's user avatar
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2 votes
1 answer
417 views

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 ...
mRotten's user avatar
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3 votes
1 answer
141 views

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 ...
mRotten's user avatar
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1 answer
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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: ...
terdon's user avatar
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3 votes
1 answer
430 views

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 ...
Colin's user avatar
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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 ...
bsmoda's user avatar
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2 votes
1 answer
3k views

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 ...
gc5's user avatar
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