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View Code? Open in Web Editor NEWPrimer Design in Anopheles gambiae and funestus considering genetic variation
Home Page: https://sanjaynagi.github.io/AnoPrimer/
License: MIT License
Primer Design in Anopheles gambiae and funestus considering genetic variation
Home Page: https://sanjaynagi.github.io/AnoPrimer/
License: MIT License
Through malariagen_data.Af1
.
AnoPrimer
'qPCR primers' is misleading, because qPCR assays can be done on genomic DNA, as well as cDNA.
We really mean cDNA primers here, as one primer is targeting an exon-exon junction, it will only amplify cDNA. This will also align with gDNA primers.
Currently AgamPrimer cannot be installed on Python 3.10 or above because of the pinning of the Python dependency.
This is particularly a problem for colab users because colab has recently been upgraded to Python 3.10.
Report exact alternate bases for A,C, G, T, rather than summing the frequency of all alts.
And suggest degenerate bases for those primers
Where/if appropriate
Currently plot_primer_ag3_frequencies()
is probably the only function worth optimising.
possible with gget BLAT to find genomic location and then malariagen_data
AgamPrimer currently depends on several packages:
import pandas as pd
import allel
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib import patches
import malariagen_data
from plotly.subplots import make_subplots
import plotly.graph_objects as go
import gget
import primer3
It would be good to express these dependencies in the package metadata so that they get installed automatically when AgamPrimer is installed via pip.
Not all of these would need to be stated directly, as several will get brought in as transitive dependencies via malariagen_data. However, not all will, e.g., at least seaborn, gget and primer3 would need to be stated explicitly.
There are several different ways to state dependencies.
If using poetry, these can be declared in the pyproject.toml file, see an example.
The old-school way to do it is by adding an install_requires
into setup.py.
So one can filter for species etc
So we can rank primer pairs on the SNP-variation score
Support to design internal oligos (for example, the base sequence for designing LNA probes)
For use in for example, taqman or lna probe for gene expression, where you have a single probe and primers.
In title of figure
Need to figure out the possible CNV orientations. this would possibly require manually providing the cnv sequence and breakpoints
how do I design a primer to target different loci of the gene?
For gDNA primers, you specify the exact genomic location in base pairs - ie. 2L:2,000,000
Is it possible to specify the exon or intergenic region when designing the primer?
for gDNA primers, yes, for cDNA primers, they will target exon-exon junctions
How can I check the primer's dimerisation probality if I have designed several primers?
Primer 3 will do this internally within AgamPrimer. If you want to see dimerisation results, you have to use the long AgamPrimer notebook, and look at the 'primer_dict' otherwise i recommend tools on IDT website
how can I specify the primers binding regions for example exon 1 to exon 4 with a single pair primer?
you cant but you can play around with the amplicon preferred size and target until it does so
In one of the exercises, SNPs were found only on the probe sequence, could this affect the efficiency of the qpcr?
It depends where in the probe and what kind of assay you are doing. you havent mentioned?
so target either is '2L:28545767' or 'AGAP006227-RA'
Remove the need to provide contig, which is unnecessary anyway for cDNA primers in which the transcript is provided.
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