Stack Overflow
Stack Overflow

Questions tagged [primer3]

Primer3 is a tool for molecular biology allowing the selection of single primers for sequencing reactions and can design oligonucleotide hybridization probes. The online tool constitutes some important features like primer detection, cloning, sequencing and Primer listing.

9 questions
3
votes
2 answers

Why am I getting this error in my Primer3/eprimer3 Mac OSX build?

I'm getting this error on my mac osx build. Primer3/eprimer3 issue: Error: thermodynamic approach chosen, but path to thermodynamic parameters not…
datz
  • 51
  • 1
  • 4
2
votes
2 answers

What is the difference between R vegan species-scores, and Primer Spearman rank correlation of species to axis?

In constrained ordination analysis, like CAP or dbRDA, researchers often want to know how much of the dissimilarity is attributed to specific species. In Primer PERMANOVA, Spearman rank or Pearson correlations of species to the axis is an option to…
Philip Haupt
  • 75
  • 7
1
vote
0 answers

Unable to install primer3-py on python3 on AWS EC2 server

I'm trying to make a streamlit app working with primer3 and the python file works fine on my PC. However I'm having trouble installing primer3-py on my ec2 server running Linux system. The command that I run is: python3 setup.py build_ext…
Shu
  • 11
  • 1
1
vote
0 answers

Phylogenetic Tree- full ITS v. partial ITS

I hope to make a single phylogenetic tree by comparing reads that cover ITS 1 or ITS 2 to reads that cover both regions (ITS1&2). (details: similar fungi, ITS region, Sanger reads of ~600bp) Is there a program/technique to compare partial reads to a…
Simone Evans
  • 21
  • 2
1
vote
1 answer

Installing Primer3

I need to install Primer3 for my research in Windows, and I really have no idea of how to go about it. I was following the instructions mentioned here. I'm getting to the part where I need to run mingw32-make TESTOPTS=--windows and I keep…
roru
  • 11
  • 2
1
vote
1 answer

primer3 web error , Unrecognized tag, primer3_core Unrecognized tag

I tried to run a primer3 web on localhost , but there was an error on the output when the pick primer. Primer3 Output: Unrecognized tag: PRIMER_THERMODYNAMIC_ALIGNMENT=1 ./primer3_core: Unrecognized tag: PRIMER_THERMODYNAMIC_ALIGNMENT=1 INPUT…
irwan Dwiyanto
  • 321
  • 3
  • 7
  • 19
0
votes
1 answer

How do I install primer3 on windows?

Problem: I need to install Primer3, a widely used bio tool that finds allows one to design primers. Attempts at resolution: I have attempted to follow their instructions for a Windows installation to no avail as it does not seem provide enough…
Thunderpurtz
  • 189
  • 2
  • 12
0
votes
1 answer

primer3_core Error: First line must be "Primer3 File - http://primer3.sourceforge.net"

I am currently using Primer3 2.3.6 in Linux. I am using the command "primer3_core -p3_settings_file=/my/path/to/settingsfile.txt /my/path/to/inputfile.txt". I also tried it in Windows 7 and it worked without any problem. However, in Linux I got the…
Michaela
  • 88
  • 5
0
votes
2 answers

Python primer3 PCR primer design

I am using this module to design primers https://pypi.python.org/pypi/primer3-py but I am getting unexpected results. import primer3 input_seq =…
crysis405
  • 1,121
  • 2
  • 13
  • 26