I have an alignment FASTA file of Dengue virus genome from NCBI. Based on that alignment i construct my own primer. After that i added my own primer sequences in the FASTA file of Dengue virus (using the same "computational language", for example: >dengueTCGTAG...>primer1GTACTC...>primer2....and so on. and then i saved the new file. After that i opened this file in BioEdit. Surprisingly Bioedit only align the Dengue virus genome and not my primer construct.
How to overcome this problem? i want to check if my primer is good or not
You select all sequences (viral genome, primer sequences) and do a Clustal-w (Accessary Applications) multiple sequence alignment alignment. This should align the primer sequences to the viral sequence
If you want to align some primers in BioEdit, you must to do following
1) put DNA fragment with annealing sites in BioEdit
2) add primer sequences
3) align each primer with DNA separately (not both in the same alignment, because the program will search for 1 site for all sequences intead of 2)
Imoptant notice: if you have direct sequence (+), you must apply function "reverse complement" to reverse primer before aligning.
Thank you Kandasamy and Andrii. Both of your answer is really helpful
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