I have F & R primer sequences and know the amplicon length and approximate Chromosome positions. Is it possible to find the target region?
Ive tried manual methods (Ctrl+F) but im getting nothing back for the long FASTA outputs. Probably due to single bp differences.
Just wondering if there was a better way of tying to find the target region. Previous papers on the primer sequence havnt given me specific locations.
Thanks
S
You can make a BLAST with your primers and the sequence most probably to amplify or a complete chromosome. Another method is virtual PCR or in silico PCR amplification, there is a lot of resources on the web, like http://www.bioinformatics.org/sms2/pcr_products.html
http://insilico.ehu.es/PCR/index.php?
https://www.ncbi.nlm.nih.gov/guide/howto/design-pcr-primers/
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
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