Assignment #5 Automatic identification of primers

In this assignment your script will take in a DNA sequence file for the C. elegans genome, and a chromosome and position you want amplified.

The idea is that the user wants to genotype a SNP at a particular position. To do this they will need to amplify a sequence of DNA around 600-800 bp long. It is also important that the beginning and end of the PCR product is at least 100 bp away. A visual schematic is included below. The first primer should be chosen between 0-400. The second primer should be chosen between 600-1000. The total product size should be 600-800 bp long.

0   400   600   1000

You should use primer3 to choose the primers and report back the best choice. Some example output is included below. I have uploaded the fasta_file for you to use as well.

[pmcgrath7@bioebb301301:~/Dropbox/NewGeneralWork/Teaching/BIOL48038803/Assignment s]$python3 Assignment7_Solution.py -h

usage: Assignment7_Solution.py [-h] fasta_file chromosome position

This program runs primer3 to identify the best two primers to amplify a given sequence

positional arguments:

fasta_file

Enter

a genome

file containing DNA sequence

chromosome

Enter

the

chromosome you want amplified

position

Enter

the

position you

want amplified

optional arguments:

-h, --help

show this

help

message

and exit

$ python3 Assignment7_Solution.py c_elegans.WS220.genomic.fa CHROMOSOME_I 4564564

ttggcagttgggaccgttta

catcgagcagtgcaggaaga

$ python3 Assignment7_Solution.py c_elegans.WS220.genomic.fa CHROMOSOME_V 4564564

tgcccaggaaaatgtgacgt

catcccccatgtcgattcga

$ python3 Assignment7_Solution.py c_elegans.WS220.genomic.fa CHROMOSOME_V 45645

ggagccaaagataacgccct

cggtaaccggcaattttgga

$ python3 Assignment7_Solution.py c_elegans.WS220.genomic.fa CHROMOSOME_III

456452

gtcctctaggagccgaggaa

ttggaaggagtggggaaacg

$ python3 Assignment7_Solution.py c_elegans.WS220.genomic.fa CHROMOSOME_IV 456452 gacaggccgaggtatgtacg

ctgcaagttctcgggcagta