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epride - easy primer design for multiple sequence alignments
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epride
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LICENSE.txt
Makefile
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test_align.fasta

README.md

epride - easy primer design for multiple sequence alignments

Description

epride is a Python tool that facilitates probe and primer design for multiple DNA sequence alignments. It does this by chopping the alignment sequences into primer candidates and aligning them back on the original sequences.

Usage

Takes a fasta input. Produces clusters of sequences and matching clusters of primer candidates.

Requirements

Tested on Python 3.5.

Depends on braceexpand, numpy, pandas, primer3 and nsearch.

Installation

git clone https://github.com/manutamminen/epride.git
make

Examples

import epride as ep

# Cluster the sequences in test_align.fasta
test_clusters = ep.Primers("test_align.fasta", id_val=0.8, primer_length=20)

# Find primer groups that cover the target sequences. Small sequence clusters or small primer
# clusters can be penalized by increasing the id_penalty and primer_penalty arguments.
test_clusters.coverage_info(id_penalty=1, primer_penalty=1)

# Print primers and their index values for a given primer cluster
test_clusters[0]


# epride also contains utility functions for simple sequence operations.
# Degenerate nucleotides are supported.

# Read a fasta file into a fasta iterable
test_fasta = ep.read_fasta("test_align.fasta")

#Write a fasta iterable into a fasta file
ep.write_fasta(test_fasta, "test_align_fasta")

#Reverse complement a sequence. Also handles degenerate nucleotides.
ep.reverse_complement("AATTYYRRWWGGCC")
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