Primer-blast impossible with multiple sequences ?

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6.1 years ago

Picasa ▴ 650

Hi Biostars,

I am trying to design primers. For this I have multiple sequences in a fasta file and I have found this program that give kind of nice visualisation:

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

1) However I cannot paste multiples sequences .. Is it normal or I am doing something wrong ?? I got this error:

Exception error: Multiple templates are currently not supported! .

2) A command line version does'nt exist ?

3) If no, do you have any recommendation for other programs that take multiple input and/or can be run by command line ?

Thanks a lot.

primer-blast sequences • 4.4k views

ADD COMMENT • link updated 6.0 years ago by Biostar 20 • written 6.1 years ago by Picasa ▴ 650

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Past thread that may be of interest: Automated Primer-Blast like funcionnality

ADD REPLY • link 6.1 years ago by GenoMax 148k

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Thanks but it is not what I am looking for. This thread talks about finding DNA sequences from a primer pair, while I want the reverse (finding primer pair from dna sequence)

ADD REPLY • link 6.1 years ago by Picasa ▴ 650

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You can use Primer3 in the commad-line.

https://sourceforge.net/projects/primer3/

ADD REPLY • link 6.1 years ago by h.mon 35k

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