SpePrimer

A script to design primers with sequence specificity

dependency

SpePrimer requires MUSCLE and Python (>=3.7) installed. MUSCLE could be installed by anaconda (conda install muscle).

Parameter illustration

The input files of SpePrimer are CDS file and blast file. CDS file is the whole genome coding sequences. The blast file is the all-vs-all results from blastn.

In the SpePrimer, we offered benchmark data only contained Ghir_A08G007090.1 and its homologs as hir.test.fasta and hir.test.blast for CDS and blast file, respectively.

SpePrimer has 7 parameters listed as below:

-gene, the parameter accepts the name of target gene which is selected for specific primer

-cds, the parameter accepts the name of CDS file.

-blast, the parameter accepts the name of blast result.

-maxlen, the parameter accepts the maximum length of the PCR products.

-minlen, the parameter accepts the minimum length of the PCR products.

-primerlen, the parameter accepts the length of the primer pairs.

-out, the parameter accepts the name of the primer design results.

Usage

python SpePrimer.py -gene Ghir_A08G007090.1 -cds hir.test.fasta -blast hir.test.blast -maxlen 300 -minlen 200 -primerlen 20 -out primer_result

Output

For the benchmark data, the output file is named as primer_result, a table with 15 columns listed as below:

forward (forward primer sequence)

reverse (reverse primer sequence)

tm_fr (melting temperature of forward primer)

tm_rv (melting temperature of reverse primer)

tandem_rate_fr (tandem repeat of forward sequence)

tandem_rate_rv (tandem repeat of reverse sequence)

inter_com (complementation rate between forward and reverse primer sequences)

self_com_fr (self-complementation rate of forward primer sequences)

self_com_rv (self-complementation rate of reverse primer sequences)

pd_similarity (similarity between PCR products of target genes and SSGs)

CG_F (CG content of forward primer sequences)

CG_R (CG content of reverse primer sequences)

start (start site of forward primer on target gene’s sequence)

end (end site of reverse primer on target gene’s sequence)

length (the length of PCR product)