Skip to main content

A small library to help K-seq users to select primers.

Project description

Primer explorer2

A small library to help seleting primers for K-Seq users .

Authors: P.Ziarsolo, V. Garcia-Carpintero, J.Blanca

This small library provides various scripts to help the user to select the best kmers for your experiment.


a) pip install primer_explorer2

b) python install

It tries to select the best 10 primers for a K-Seq experiment and predicts the outcome of all 10 primer combinations.

The outcome consist in two file:
    * An excel file with some stats for each primer combinations.
    * A database with the predicted pcr products for each pair combination. This can be use as input for other provided scripts.
You can use the script to look for primers in different ways. 

You can choose the length of the primer. The bigger is the length of the primer, less sites in the genome will find, thus generating less pcr products
You can define regions in witch you prefer to have less primers. P.ej: heterocromating, repetitive...

It generates a bed file for each combination of primer pair in the pcr_products pickle database.

It draws the insert size distribution of the predicted pcr products.

Given the prediction in bed files. It counts how many predicted pcr_products are in the gff features. By default in only counts pcr_produts in exons and genes. It can be changed.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for primer-explorer2, version 0.5.4
Filename, size File type Python version Upload date Hashes
Filename, size primer_explorer2-0.5.4.tar.gz (153.9 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page