epride - easy primer design for multiple sequence alignments
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.
Takes a fasta input. Produces clusters of sequences and matching clusters of primer candidates.
Tested on Python 3.5.
git clone https://github.com/manutamminen/epride.git make
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 # 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")